I would have a hard time shedding tears over dead bugs myself. The problem I have with using weapons of mass destructions is that it invites retaliation in kind. When the Kilrathi did it to us with with Strontium-90 nukes and bio-weapons, we had no compunctions of hitting back with the T-bomb.
Similarly, if we start using them against the Nephilim, the bugs could too. Given that they know where our homeworlds are (but we don't know where theirs is) and that their wormholes give them a very good chance of jumping past any defenses we can set up to reach our homeworlds, do we really want to escalate the conflict to that level?
Best, Raptor