She fell into despair. Because of life? No, because of Madoka. Even though she created a world with Madoka in it, Homura still fell into despair. Was it because Madoka doesn't remember her completely? No, this isn't the Madoka she has loved. This Madoka was different, completely different. The Madoka she loves is the Law of the Cycle, not a Puella Magi.
Her despair was complicated. Changing from a 'Puella Magi' to a Witch involved herself and Madoka. Seeing Madoka turn into a pool of pink and then pounding herself. It was confusing, for she was sure Sayaka didn't go through that much pain while transforming into a Witch.
But maybe it's for another reason. After all, she was the 'irregular' Puella Magi.
She just lost herself, she's finally a Witch. But her feelings are still intact, why? Maybe it's because, Madoka's here? As the Law of the Cycle, not the Puella Magi, yeah, that's why. Homura's not completely lost; she's still here, just in spirit. Kind of like, Madoka. Yes, because of Madoka, she isn't lost.
But she can't die here, not until she sees that Madoka one last time.