It's surprisingly hard, given the circumstances. What could they possibly use, unless they attacked before she stops time? Antimagic may work, if it's in a bubble around a girl. Either it kills the timestop when Homura gets close, the girl gets to move around inside the time stop unaffected, or Homura just shoots her with a sniper rifle before either of those things become relevant. Having some sort of thread-shield that's immune to bullets and would connect to her if you got close might do it, but that's rather specific. Mind control, if applied beforehand? Precognition, to know not to show up in the first place? Illusions or invisibility might help you survive too.
Considering that all magical girls share a common, easily exploitable weakness in their Soul Gems, the only real way to stop her would be some way to render it immune to bullets and just outlast her reserves. Most characters in Mitakihara are pretty much the cream of the crop when it comes to esoteric magic, other than Kyouko and canon-Sayaka.