I'm no anime/manga expert, so pardon if some of this doesn't make much sense!
I find it interesting that in this series, the heroine doesn't live up to its title till the end!
I HIGHLY suspect that anime episode 9 was actually a compilation of several time-playback attempts by Homura and not a single "episode." Well, having just skimmed the anime and manga, the questions I have is:
Is Homura's time-traveling limited to periods before she met "Incubator"? If so, then episode one isn't the "baseline timeline" for pre-magical Madoka, but rather what was played out in timid Homura's first encounter with Madoka in episode 9. This was the (next to) best time for "future Homura" to hammer Madoka with the truth.
Maybe it's me, but unless the Soul Gem can inhabit what Magic girls could say, Homura isn't trying hard enough to spill the beans about Incubator to Madoka and Miki. A good display of her magic powers would've been pretty convincing to prevent any contract signing. Plus -- if it's implied that Homura can drag someone into time traveling with her that would've been more than additional proof. If so, and they together could even persuade the pasts of other magic girls all over, they could starve Kyubey's witch supply -- and plans.
One way the girls, once turned Magic Girls, might "escape" the witches fate would be to form a kind of "taint rotation ring" among them; Girl A transfers her Soul Gem's "taint" to Girl B to wash hers clean of the taint then Girl B passes hers to Girl C, then whoever's the last one passes it back to "clean" Girl A, etc. One girl always has the most taint while the others are "clean." Also, since you mostly get tainted by despair and depression, it would seem that the Girls should take up more cheerful rewarding careers, even motherhood since maybe motherly love is a great taint buster.