Vexen does perhaps imply that Xehanort might be able to exert control over any of his members "he is one of the chosen so he can't disobey". Which makes sense if Vanitas was able to paralyze Sora just because Ven's heart was inside him, and Ansem-Riku did the same to Sora using Kairi's heart in conjunction with the hearts of the other princesses....it's really not a stretch to believe that by accepting part of Xehanort's heart that he can just exert his influence over them if he so chooses. Of course I think it's more than that, a heart in someone isn't just like a person possessing another person.
A heart is memories, emotions, and connections the experiences that define us and shape us into who we are. When Xehanort puts a piece of his heart into people he's putting his emotions, his memories, his connections and experiences into them. As a result anyone who is half Xehanort at least partly shares Xehanort's desires. Xehanort's possession isn't really much of a possession it's more like...an ability to sway people to his side through force. You've heard of the old saying "winning over the hearts and minds of the people" which is where a person with significant enough charisma can sway a person into thinking like them or acting on their behalf by use of words/speeches/examples/etc... When Xehanort puts a piece of his heart into someone he's really just sharing his ideals, his beliefs, his feelings with them but instead of willingly agreeing with them they just sort of instinctively do now because his ideals, beliefs, and feelings are now mixed in with their's. Sora achieves a similar effect on people but his is always effect is always consensual and he becomes a part of their hearts metaphorically rather than literally...okay in some cases literally.
Which means Xehanort's possession is less him hopping into a body and taking it over, but it's more like he's creating a new person. His experiences meshes into the host's and since the experiences are what define a person they internally have to reconcile themselves into something that's not quite them or Xehanort but a unification of the two. With Riku as an example we saw how a perfect unification made the two virtually indistinct as Riku-Ansem, until the Xehanort part of him wanted to do something so in opposition of what Riku wanted in regards to Kairi and the two of them had such distinct feelings over the loss of Sora...that they literally couldn't reconcile. The two went from an almost perfectly meshed union into two very distinct conflicting sides, the conflict split them spitting out Riku's heart from his body as result. Even after Ansem's destruction he remained a permanent part of Riku, and the two openly viewed themselves as two halves of the same person where in Ansem embodied Riku's dark side and in reverse Riku effectively embodied Xehanort's light side. Creating a constant clash were eventually Riku consumed that part of himself, reconciling and making himself whole, and thus in turn freeing him from the shadow of Ansem.
So now looking at that I think it makes Saix's actions more clear. Part of him is Isa the former friend of Lea who wants to reunite with his best friend and make amends for his jealousy by bringing back Lea's lost friends, and even recognizes that his jealousy was irrational and based on hurt feelings he had tried to pretend didn't exist. But the other part of him is Xehanort the man who wants the war, who has shown time and time again to be vindictive and spiteful to even those he considers friends, who killed his best friend over their differences. The Saix we know is neither Isa nor Xehanort but a union of the two and like Riku it appears Isa meshed better with Xehanort, perhaps the jealousy and hurt towards lost friends created a common anchor that made it easier to draw on Isa's darker impulses. Which leaves us with a conflicted man, one who wants to make amends to his friend but also very much wants to beat his face in and Saix ultimately reconcile these two parts by helping restore Lea's friends while also psychologically torturing him and fighting in the war. Meanwhile someone like Vexen the only real common ground for Xehanort's personality to mesh would be his ego and scientific curiosity, so he happily rejoin the org and produce replicas for Xehanort because it would satisfy both those things but would let him work towards his real desire which was to bring back lost people in order to make amends.
Another good example of this is Dark Aqua who is "Aqua under Xehanort's influence". She is very clearly still Aqua but Xehanort's darkness had meshed into her, drawing out those dark feelings she keeps suppressed. Abandonment, anger at friend, loneliness, the sense of a friend holding you back from greatness, etc... these are all dark feelings Xehanort shares and would create a good anchor for her darkness to mesh with his. In a twist of irony Aqua may actually mesh better with Xehanort than Terra does, which is why Aqua shows no real resistance to what is going on because it's all stuff she wants to do and feels just being magnified by having twice as much of it now. While Terra all he really had was dark deep anger for Xehanort to latch onto so even when Xehanort joined with Terra the two didn't mesh much, Terra remained an almost wholly distinct person fighting Xehanort at virtually every turn. In a way it's almost like Aqua is basically female adult Riku while Terra was adult Sora, the similarities between the opposite were based more in circumstance/role than personality. Which is why Terra and Sora have this problem of wearing their hearts on their sleeves, rushing in, a desire to be the hero, being a tad gullible, and having a lot of anger that bursts forth as an overwhelming dark power. Meanwhile Aqua and Riku both have the problem of keeping everything bottled up, being a bit socially awkward and mistrusting, trying to be the role model and carry the world on their shoulders, and just in general wear themselves down to nothing.
So yeah I think the handling of Saix made a lot of sense and the answer to the question of "why didn't he help stop Xemnas" boils down to simply that part of Saix didn't want to, the negative spiteful part that Xehanort's essence was magnifying prevents him from truly turning on Xehanort. But he was still enough of Isa that he could be self aware, recognize his mistakes, and try to make amends in a way that also didn't conflict with that other part of himself. But that's just my interpretation of the whole thing really.
but thats where we're at lol. 
(which is a pretty cool detail).
