You forget that Homura has spent over a decade going through the same month over and over again. She has known Madoka for almost as long as she has known herself. Madoka was even the one that told Homura to stop her from making the stupid decision to become a magical girl right before she had Homura mercy kill her.
Homura became utterly monomaniacal about stopping Madoka from making that wish that why she was doing it became a secondary concern. How Homura treats Madoka's actions makes it fairly clear that, even after all that time, she still didn't understand her any better; it simply reduced her to the state where her monomania was the only thing keeping her from loosing it completely.
When was it established that Madoka was happy not existing? She is happy not being able to spend time with her family or that her family doesn't even remember her? I highly doubt that. She chose to sacrifice herself to save magical girls from becoming witches, just because she doesn't regret that decision doesn't mean that she is happy. Besides does Homura not deserve to be happy?
It's not established that Madoka's happy in Homura's fake world, either. One thing we see throughout the series is that Madoka's at her worst when there's nothing she can do.
How is Homura any different than Madoka? Was Madoka's universe not simply forcing Homura to live in a world she dreamt up? The one where she succeeds in her all-consuming quest to prevent the creation of witches? Homura repeated what Madoka did in order to fix all her mistakes.
What Homura did is almost impossible to differentiate from holding someone in a cellar "for their own good". Madoka's actions are more akin to jumping out in front of a car to push someone else out of the way. And, like I mentioned, we can see throughout the series that, if Madoka was in that position, she would never be able to live with herself if she didn't make that leap.