>>2819136As Urobuchi has said, the inherent cruelty of the story is that at no point did Madoka realize what Homura had done for her sake and as such never took Homura's desire into account. Rebellion seems to have corrected this by effectively forcing any course of action to have to go through Homura. Due to Homura's power, the problem is more or less impossible to solve with violence, forcing Madoka to find resolution in a mostly hopeless situation.
I also find that it is very difficult for Madoka to cause a big stink. To deny Homura and her wish forces Madoka to deny the suffering that was necessary to grant her own wish. One can say that Madoka's wish matters more because it utilitarianism. And to that I say fuck, off Kyubey. Like you said, the spirit of Madoka's wish was that everyone's wish be granted. And for Madoka to say 'lol except Homura's because it interferes with mine' would be increadibly selfish and grossly out of character
I'm biased, but I honestly feel that to be a more important story line to resolve than Homura coming to terms with granting Madoka agency.
