I don't think we should give up hope for a possible sequel right now. We have never been hinted about the white and black puella magi 's existence in the anime but, they appear here. During ep. 10 we saw that though all timeline diverged but there isn't that much of a difference. The situation just played differently. Unless, Homura ( the differing variable in all timeline) outsourced outside help which spiraled out of control then, I have a hard time seeing this a prequel.
Besides, according to the synopsis, - Homura, Mami and Kyoko are not supposed to cross paths. But, it seemed in the timelines that Homura traveled to or have been shown they are suppose to cross paths. Besides, its suppose to test their existence or change the fate of the puella magi according to Vol. 1. But, unless its after Madoka's rewrite then most of change would be gone.
Anyway, protecting Madoka's peace esp. in context of Homura can be protecting Madoka's normal everyday life or protecting Madoka by encouraging her not to contract. Or it could be post-series Homura's wish to protect the world that Madoka died to protect.
I do agree that "past timeline" does damper the chance of its sequel a bit. But, thinking of all the other details makes the chance of it being a prequel also sketchy. Anyway, though I dearly wish that its a sequel, I also want to see the timelines that Homura traveled to. So its a win-win situation.
Though, if it is a prequel this would give hard evidence that there are more than five timelines...
