We never heard of a ban or other expression of disapproval over the use of chemical weapons. Probably those are considered much more humane than, say, kinetic weapons or death rays, and would be the preferred sort if not for the pesky opponents so often donning gas masks or gas-stopping shields.
What I found more surprising and perhaps objectionable was the introduction of the concept of a "Maquis planet". Until this episode, the Maquis had been a group operating out of certain colony worlds but certainly not forming any major part of the population - or in other words, the inhabitants had expressed no formal association with the movement. The sudden emergence of "Maquis planets" makes it much easier to use global-scale weapons, which is a great convenience in terms of drama, Starfleet politics and Sisko's tactics alike...
Jean Valjean was imprisoned because he stole a loaf of bread.
...Whereas Eddington stole the whole goddamn bakery, leaving millions starving, all so that he could bake weapons for himself.