Punching or bashing them kills them (I try it with the bloodbugs down by the river as well and get the same result). The flies are an issue because, as far as I can tell, flying creatures can't be knocked out using the mod.
I dump the unconscious roach near the Vault exit and ride the elevator to the surface, then make my way to Sanctuary Hills, where I discover two little hovering problems: Bloatflies, and Codsworth.
