Are you seeing evidence of the bacterial infection in the guppies?
From what I gather, you only seen the bettas with the infection correct?
If you aren't seeing symptoms in the guppies, then I would stop the treatment. Their behavior is more likely caused by stress than disease. And medicating them will only contribute to that stress if they aren't infected. Keep their water clean, keep a close eye on them, and let them settle in.
I have found that
aquarium salt is quite useful when bringing in new guppies. And it can also help with bacterial infections. Aquarium Coop has a pretty good guide on how to use it.
I don't think the bacterial infection is the root of your troubles here... unless of course you are seeing direct evidence of it.