[AquaMethod]

Originally Posted by Hooves

It's probably the thought that Kyuube is bringing more and more magical girls in this world where one's life is at risk. Homura (being sensitive as she is) wants to stop this from ever corresponding.

Spoiler:

It's also possible that she was tricked or forced into becoming a Puella Magi like Mami was, and doesn't want the girls to actually make the choice to become one. Which could be why she wouldn't tell Madoka her wish with Kyubey around.