Assumed that they are doing something bad? I just think your wording is off on that one since assuming someone is doing something bad is the same as assuming someone is doing something good i.e. Sora.
Well, maybe assumed isn't quite the right word. What I was getting at was, even in the Demyx case (which is the only truly hard case out of all of them, because the other Organization members were clearly a threat and Sora wasn't seeking them out, apart from Xemnas), it doesn't look (to either us or Sora) like he's there just to ask Sora whether he wants to go out for sea-salt ice cream. He appears in the middle of an invasion, is apparently surprised that Sora is there, and is part of the organization that's carrying out that invasion.
It seems clear that he's there to do the same thing as the rest of the Organization, hence, he's a threat. He might not act or talk like one, but Sora's been told that the Organization would try to confuse him.
Besides, fighting isn't Sora's first response anyway. He's not exactly nice to Demyx, sure, but it could be a way of figuring out whether Demyx is acting or not. And Demyx's responses aren't exactly reassuring.
Sora says, "I bet you can't even fight." Demyx's response is, "You can't judge anyone by appearances," which sounds a bit like a veiled threat (though, it's probably more of a bluff, considering his reaction to Sora's response). Sora responds by preparing his Keyblade - but drops out of the defensive posture once Demyx says, "I told them they were sending the wrong guy." He and Donald then try to call Demyx's "acting" out - "Right -- no hearts!" and "You can't fool us," to which Demyx brings out his own weapon and starts the fight.
To Sora, that probably looked like, "Well, I guess the act is up" more than "I don't want to fight, but you're making me." Which would be even more proof towards Yen Sid's words.
The thing is, we know that Demyx was meant to be the "nice guy" of the Organization, so it's easy to think that he really meant everything. But even with our extra knowledge, it's not clear that the entire thing wasn't an act on Demyx's part, so it's not fair to expect Sora to think it isn't.
Anyways Sora isn't even confronted with the other Org members until late in the game(besides the one instance in HB). What the hell we they doing in that time? Plotting? Yeah but certainly not attacking him. Ooh they have weapons, well of course they have weapons! You think an Organization ruled by a madman isn't gonna have weapons?! Org: Either they attack this boy or get attacked by Xenmas. Sora: Either he must eliminates these people or others might get hurt. No where in there on either side is a thought of maybe I can do this instead of that, both are just see things in one way and that is that.
Well, no, they weren't attacking him at that point, because they still needed him to kill Heartless and complete their Kingdom Hearts. But things changed at the end, and in a very significant way, before any of the Organization members post-Axel died.
Saix tells Sora right out - "Organization XIII has no further use for you." Which means, from that point out, they want him dead.
If someone wants you dead, and force you to fight them to the death, it's not evil if you end up having to kill them. It's self-defense. Once it gets to the point where Sora either has to fight or die, it doesn't even matter how noble the Organization's motives are, Sora needs to be able to protect himself.
And the "attack this boy or get attacked by Xemnas" thing doesn't work - it's pretty clear that most of the post-Axel members have their own reasons for doing it. Xigbar seems all too happy to carry out his orders (or at least, that's what "You really shouldn't have betrayed us. *smirk*" implies to me), Saix clearly takes some kind of sadistic enjoyment in the idea of killing Sora ("How I've waited to hear that" when he gets his orders), and Xemnas isn't acting on anyone's orders besides his own. Maybe Luxord is, or maybe he isn't, but he's not willing to talk about it either way.
Sora never had the thought of letting them live cross his mind and like you said once he is in the fight he can't really stop or more or less doesn't want to stop. I have never seen Sora stop attacking while in a fight for moral reasons, even when Riku(in black cloak) tries to aid him in Land of dragons he attacks and doesn't look at what Riku was really doing(he was killing the heartless).
It's not really Sora's fault that he doesn't stop - I don't think "he doesn't want to stop" is a fair assessment. He can't stop, because if he stops fighting and the other person doesn't, he'll be killed. It's pretty simple, really. And Sora stops in the Riku fight once Riku shows that he doesn't want to fight anymore, so it's not like he can't stop himself at all.
As for "never having the thought of letting them live cross his mind," well, I don't think his intentions ever were "take out the entire Organization" (that was more DiZ and Riku's thing. It's Riku, not Sora, who's the one who says "We must defeat Xemnas. He's the Organization's last survivor," the phrasing of which implies that Xemnas must be defeated because
he's the Organization's last survivor; this is complicated by the fact that he let Axel live earlier, though Axel was no longer fighting for it, so who knows) as much as, "stop the Organization from hurting people." If he was put in Riku's situation of being ordered to kill a defenseless Namine and Axel, he wouldn't do it, either.
No, you see he is first told that the nobodies shouldn't exist and in turn are bad with that information Sora goes out and does his "heroic duty" but like you said the one piece of evidence is Axel's change before he died so if Axel was able to change then why not the other members? The point is that Sora thinks that all nobodies and heartless are evil and need to be destroyed when it is clear that they can be either or.
Maybe they could - but, not long after he learns this piece of information, the Organization changes their goals to include Sora's death, which makes it highly unlikely that any of the members would be willing to change because he was nice to them or something.
As for thinking all Nobodies are evil... well, he certainly didn't show that towards Namine and Roxas when they appear out of Kairi and him. Or when he first learns about Roxas - he says it's crazy that he'd have a Nobody, but that's only because he forgot about getting turned into a Heartless, not because he can't believe something evil like that came from him. And he wishes he could meet
Roxas. Not the kind of thing he'd want to do if he thought all Nobodies were evil, right?
Well if the boy would think for a second of why this random guy called me a traitor I wouldn't be angry. I want to see some damn thoughts pass though this kids mind, I don't like the way Sora just brushes off important issues like "what is like to not exist or not have a heart" or even "why is this man with a eye patch and a scar yelling at me". No Sora just goes "Huh?" and then "RAWR!!"not that he doesn't have a right to but could he at least exhibit some sign of intelligence.
He does wonder. I think he thinks Demyx is just an oddball who has the wrong guy at first, and Demyx ignores the, "why are you calling me that" so Sora has no reason to stop thinking this. He's just as confused when Xigbar calls him Roxas, and he does try to ask - he's just a bit late about it, though I don't think you can blame him for it, considering that as soon as Xigbar shuts up about how Sora's pathetic compared to the past Keyblade wielders, he's trying to kill Sora, and doesn't stop until he's already dying. Luxord makes it quite clear that he doesn't want to answer questions ("I'd rather we just skip the formalities.") and doesn't call Sora Roxas until he's dying anyway and it's too late for Sora to ask, and by the time he gets to Saix, he's already been refused the answer three times so he probably thinks he just isn't going to get it from the Organization. It's not like he's wasn't thinking about it.
As for not thinking about what it's like not to have a heart... well, I wouldn't want to have to think about it if I were him, either. Though it's not like he never considers it - he does when thinking about the Experiment in Halloween Town, who also only wanted a heart ("Hmm... when you put it that way, I sort of feel bad for it"), and I'd be kind of surprised if he didn't make the connection with the Nobodies. And he does seem to pity Xemnas for not knowing what it's really like to have a heart - look at his expressions when Xemnas is fading in the first armor-Xemnas fight, when he says, "[The heart]'s full of all kind of feelings. Don't you remember?" Sora's tone almost sounds pleading at the last part, and his "we saved the world" victory laugh thing seems a lot more half-hearted and forced than his "We did it!" after he and Riku beat Xemnas for the final time (...granted, fighting someone to the death four times in a row probably does a lot to make you lose your pity for them). Not what you'd expect if Sora didn't give any thought to what Nobodies felt like.
I have not said that the Org members aren't evil that is not the question here my point is that with the motives they had shouldn't Sora have at least considered thinking of something else besides destruction? Yes they do bad things to get what they longed for and in way so did someone like Riku. Riku joined the dark side to try and help Kairi and was manipulated just like the Org for something he wanted even if it meant betraying Sora or even hurting others, should Riku have been killed cause he was bad? No because he is your friend who is being controlled, right? Wrong because if you admit that someone can turn from good to bad then why not the opposite? Sora never sees or even thinks of that and that is my problem, albeit that Riku's cause wasn't as extreme but it still a very similar case. Not that he is evil, not that he is good but that he is a prime example of "attack now and ask questions later"
But Sora doesn't have another choice, really. He has to go to The World That Never Was, because Kairi's being kept there there, and Xigbar attacks him because of it. Xigbar wants Sora dead, and attacks him first. There's no alternate solution - Sora either has to kill Xigbar, or he dies.
Considering the fact that you called Xemnas a madman, you clearly think that he needed to be stopped. So, it's heroic for Sora to continue on in the castle to look for Xemnas, so he can stop Xemnas from destroying other worlds and hurting people.
This, of course, forces Sora to run into Luxord and Saix before he can move on and find Xemnas - and, like Xigbar, the first thing they do when they see him is try to kill him. No choice, again -just fight until they can no longer attack him, or get killed.
Any course of action that Sora could try to take with the Nobodies requires him to move through that castle and come face to face with the Nobodies. And the Nobodies will take any face to face meeting with Sora as an opportunity to kill him.
I'm not seeing what other options there are for him to consider, really.
As for Riku... well, yeah, he's pretty much in the same boat of "doing bad things for a not-so-bad reason," which is why it's fortunate that it never ended up coming down to kill or be killed because Riku had a better sense of when to run away. And I doubt Sora would have attacked the Organization members if they decided to run, apart from Xemnas who was the main threat anyway. He certainly didn't seem worried about the fact that Demyx decided to leave the first time, in any case.
Do you realize how many thoughts the brain can make in a mere 10 minutes. Sora doesn't have to worry constantly about Riku and Kairi he just chooses to dwell on that one thing which probably just adds more fuel to the fire instead of thinking about other issues.
Was Sora really wondering whether Riku and Kairi were alright when he was doing Struggle? Probably not. Was he thinking about them when he was in the 100 acre woods? Maybe maybe not. Is he thinking about them in between the times of going to a new world/leaving one? Possibly. The list goes on and on (which doesn't really prove anything mind you cause he can make time) but the fact is Sora has time to think about other things and question stuff but he just chooses not to.
I'm not saying that was the only thing he was thinking about. xD But, when he's doing Struggle, or in the 100 Acre Wood, he's not thinking about the Nobodies, either. Most likely, when he's on different worlds, he's thinking about his friends on that world more than anything else - or, fighting for his life against the various Heartless and Nobodies who appear.
And the gummi ship times don't really count, either - he's forced to fight for his life then, too, considering the fact that the Heartless and Nobodies have gummi ships of their own and want to destroy his. Not the best time to be thinking about what it's like to be lacking a heart.
I think it's pretty understandable that he doesn't think about what the Nobodies' motives are or such.
Sora not doubting Yensid is understandable for a follower but not for a hero who has to deal with these "conflicting" issues that can cause one to think about what it means to exist and whatnot. With that said I still hold my position of neutrality.
I don't think a lack of deep thinking is enough to disqualify Sora from being a hero. Sora's a hero because he's willing to risk his life to protect his friends, not because he's the brightest bulb in the box.
And I still don't see much conflicting. Demyx, if you're not willing to interpret him charitably, seems like the perfect example of what Yen Sid said about Nobodies trying to trick people into thinking they have hearts. Xaldin, Saix, Luxord, Xigbar, and Xemnas don't demonstrate a single action that is not clearly trying to harm either Sora or someone he cares about. The only thing that conflicts this is Axel - and he's not only against the Organization, but acts completely different than any of them in the two times that Sora sees him.
And Axel himself seems to want Sora not to question that the Organization is wrong, considering that he refuses to tell Sora that they're collecting hearts to get their own back, but that's not really relevant since Sora doesn't know that.