It raises the risk of retaliation in kind, and it's an afterthought. We know the NTF committed acts of genocide against the Vasudan people, and yet both the Vasudan and Terrans of the GTVA in FS2 explicitly state they will follow the rules of war of BETAC.
Cheating those rules is a thing that happens in war, you have SOC conducting assassinations in the like. But a magic chemical attack on a planet with several billion people is not going to get suppressed in its information. It would trigger exactly the kind of civil unrest and turmoil the GTVA is terrified of.
It's not a military reference, but a musical one if you're curious.