Homura's time travel is really fucked up. First of all, when she time travels, whatever Homura that should exist in that world ceases to be and is overtaken by looping Homura. She also creates a new world period, and after she leaves, that world still stays around. Remember those timelines where Homura left when Madoka becomes Kriemhild Gretchen? Gretchen absorbed everyone on earth into her barrier with nothing to stop her. Timelines where Madoka or the others die in some way? Their family and friends are mourning them. Homura has actually made a bunch of bad end worlds. In the original timeline, Mami and Madoka died, but at least Walpurignacht was destroyed.