Excuse me my english, but I really want to say it.
I've been wondering about it for quite a while too. I found a few answers.
First of all, Sora have been told of the Organization like of an enemy. So it was Yen Cid who started this

But there also was Ansem the Wise. He as DiZ and the King met in “Chain of Memories”. In that time Ansem was “obsessed with thoughts of revenge” and -- I believe -- made everything he could to incite Mickey against the Organization (it was pretty easy after the events in Castle Oblivion). I believe it was Mickey who told Yen Cid about the Organization, but in that time he was holding to Ansem’s stand. Furthermore, why Ansem would like to awake Sora? Because he planned to use him against the Organization. Well… he succeed. He got Namine, Riku and the King to take part in that plan too. So it turns out like Sora had been manipulated the whole time.
But there’s one more important thing to speak about. That’s Organization actions. First of all, they started all this by eliminating Ansem the Wise. Yeah, they did it because they want to proceed with their experiments. But I can’t see anything good in their intentions. They weren’t doing for the public benefit. I believe it was because of Xehanort’s resentment. And -- they knew it was dangerous! So when they lost their hearts they just got what they deserved.
Things went worse when they became Heartless. Of course there is something pitiful in their situation, but there’s also one thing that doesn’t let me blame Sora: they lost their morals. Creating heartless, stealing stuff, killing and kidnapping people (Kairi, Belle…) became something usual. They don’t doubt in their right to do it, that’s why Sora don’t have to be urge forward by Ansem. He is candid facing them, in each case I can see his motivation (exept maybe for the second Demyx… but one more time, it’s not Sora who attack first). Even in Xemnas case: remember guys shouting “Xemnas! No/Don’t do it!” in the end of KH2? It was because of Kingdom Hearts. It doesn’t look like they were worrying about temselfs. Can’t find any proofs right now, but I’m pretty sure Xemnas’ influence on KH wouldn’t be positive.
Of course Organisation could avoid the confrontation, especially after Sora killed a few members in CoM. Well… of course they made a lot of stupid things like showing up in the Bailey, but… they are the main antagonists, Kingdom Hearts is an JRPG… did they really have a choice?
Just one more thing to add: I don’t believe they really could come back to normal. It’s like Heartless: they collect hearts, but can’t use them. Roxas and Namine could become whole, but why? Because Sora and Kairi have no darkness in their hearts. Speaking about Organization, their Heartless vanished (at least, things in Ansem’s reports were kind of desperating),while Xehanort’s heartless have been killed by Sora. Well, this one guess is IMHO, but I think this theory is quite lively.
(Yeah, I have to mention: I don't hate the Organization. On the contrary, I am their fan. I just want ot be unbiassed).
Thank you for your patience ^__^”