As far as I know the bug hunters are people who have an unnatural desire for vengeance against bugs, and will do anything for that purpose, even subverting their fellow humans, for that goal. Their reason for attacking Mushibugyo was because she was a bug monarch or something and was the child(?) of the eternal bug.
Why then, now that there are probably no more bugs in the magistrate, are they wanting to weaken them, despite having aligning goals. Are they just terrorists with a false noble goal in order to fool convertee?