In re-watching the movie yesterday, I did get the impression that Homura was pretty startled by the Flower Fields conversation.
There's a definite sense of "Oh noes! Madoka is probably badly suffering as Madokami!"
So I think that Homura is at least completely sincere in coming to this belief. Alas, I also think she's mistaken, and read a bit more into Madoka's words than she should have.
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