I agree with you in part, had this been the end of Rebellion, I could live with it since it would be definitive to conclude on this point. That said, what The End of Rebellion promises (at the least) is some kind of confrontation between Madoka and Homura. I hate to say it, but I do want to see that clash because at the heart of it is the source of the problems, quite a few assumptions between the two build on the fact that they know LITTLE to NOTHING about each other.
That does need to get hashed out at some point, plus... as much as it would lead to another bittersweet ending, Puella Magi Madoka Magica was build on a hopeful, bittersweet ending, it would be rather fitting to end at that point again.