I can see it still becoming bittersweet. They don't have to follow the theme of hope as shown ala Rebellion.
Homura could still be offered salvation in the end, but will probably reject it. I can see Homura killing the girls eventually if they continue to try to reraise Madokami which would send Madoka in to a fit of sheer rage.
Its inevitable that Madoka and Homura will become enemies, I doubt it'll end in the sweet manner that could have been in Rebellion. But Gen doesn't believe in the "Happy ending". The "Not yet" track implies the story isn't over just yet and that another tale is about to begin.
Not to mention I feel that i should bring up that Homura is in a constant clash of pleasure and pain. she hates herself for what she did but at the same time revels in it. She is unhealthily obsessed with Madoka, and now she has the means to keep tabs on her 24/7. She will have no qualms about killing a few people if she must, however everyone is already close with madoka in some way or manner. So doing so is out of the question if Homu doesn't want auto ascending Mado and an immediate clash of blades.
I don't wanna say I have no hope for homu, I just won't be expecting much of her.
Besides we all know Mami is best meguca.