I like most of your theory but the way you wrote it makes it seem like this will all happen somewhere mid game and Sora will be on his own for the remainder of the game till the finale. I don't really see that happening. I actually think everything we've seen in the Keyblade graveyard is pretty close to endgame.
But in any case I think Sora will be 'alone' for the final showdown or penultimate showdown. I doubt many if any of the big names are truly dead.
I was genuinely surprised and concerned to see Aqua fallen to darkness in that trailer, but the more I think of it the less I think it will matter. Pretty sure Aqua, Terra, and Ven are getting a happy ending one way or another.
I actually really like the idea of a Namine/Data Sora/Repliku trio. It just seems to work. They are all misfits.
I can see the Vanitas argument in a way too, but I really don't want him to 'go good'.