This really highlights what I'd say is Homura's tragic flaw: she's so obsessed with protecting Madoka she's stopped seeing her as the person she is, infantalizing her in her mind to the point of overruling Madoka's own decisions with only the tiniest scrap of "justification". Homura's chained to the wall and unable to reach Madoka for shackles of her own making - the artist really does know how to pick his imagery.
No offense, but I feel like if there's one thing Season 1 showed it's that the entire cast (minus Homura?) is incapable of making decisions for themselves. I'm not justifying Homura brainwashing everyone, but in a way Madoka, Kyoko, Mami, and Sayaka do need to be infantilized because none of them (not even Madoka, though her heart is in the right place) have shown the maturity necessary for their powers.
If I had to choose between living in a universe run by Homura and a universe run by Madoka, I'd choose a universe run by Homura hands down. Homura may be ignoring everyone else's opinions, but I think she's also a lot more capable and mature. So I don't necessarily see her running the universe and making all the big decisions as a bad thing.
