Frankly, as much as I think the Maquis are immoral and stubborn, I was sort of disapointed to see that Sisko faced no repercussions for using biological weapons on a civilian population. I think that with biological weapons on civilian populations, it's pretty black and white: It's immoral.
Though, I see often in this thread people claiming "starfleet" used the weapon. Just because we didn't see Sisko getting grilled on screen doesn't mean that Starfleet endorsed his idea of using WMDs. All we could really tell by starfleet command's reaction was that they were satisfied to see Eddington in a UFP penal facility. Even with Sisko being a Starfleet captain, I don't see how this demoralizes (in the sense of weakening one's morals) Starfleet as a whole.
Regardless, I did enjoy to see the WMD's launched at the colony, just because It was interesting to see what incredible measures Sisko takes when under a vendetta.