HOMURA DID NOTHING WRONG
I never saw the point of Rebellion. Your girlfriend is now a love goddess, and yeah, people don't remember her, but you do, and she's a comforting presence, and the Universe is still being saved, and the Incubators are proven wrong, and yeah, there's fighting and suffering, but it's way less and only enough to give life meaning. So, let's destroy all that, destroy your reputation and become a villain, because, hey, you can't wait until you die by natural causes and can reunite with her. I really think Homura did everything wrong. I realize that's not a novel perspective. Homura was the only non-ditzy character (sorry, Madoka) who was a pure hero, period. Until this point.
The only way to explain it for me is the endless Groundhog Day crap made her, finally, snap, and the movie was The Madness of Homura.