I'm not so sure about that. If the ships can communicate with each other, they can decide to gang up on the humans and prevent the humans from shutting them down. The humans really don't have that much power over the ships; the ships just haven't done anything to limit the humans' activities yet. That could change at any time.

If the ships wanted to be really nice, they could just beam the humans down to a safe planet and take off into the interstellar void and find themselves a new home.