Bombings, hijackings, piracy, genocide--the Maquis were far from civilians ... and innocents.
But not everyone in Maquis colonies participated in those things. Remember, Sisko targets a Maquis "colony." Not a Maquis raider base or a weapons depot - a colony. In other words, he chose a civilian, not a military, target.
Sisko says all this explicitly:
EDDINGTON: (hologram) What are you really up to, Javert? Do you expect me to believe that a decorated Starfleet officer, the pride of the service, is going to
poison an entire planet?
SISKO:
That's exactly what I'm going to do.
EDDINGTON: You're bluffing.
SISKO: Am I? Commander, launch torpedoes. Commander, I said launch torpedoes!
WORF: Aye, sir.
(Two lights impact the atmosphere, and it starts turning yellow.)
KIRA: The trilithium resin is dissipating throughout the biosphere. The Maquis are scrambling their transport ships. They're starting to evacuate.
EDDINGTON: Do you realise what you've done?
SISKO: I've only just begun. I'm going to eliminate every Maquis colony in the DMZ.
EDDINGTON:
You're talking about turning hundreds of thousands of people into homeless refugees.
SISKO:
That's right. ...
EDDINGTON:
But think about those people you saw in the caves, huddled and starving. They didn't attack the Malinche.
SISKO:
You should have thought about that before you attacked a Federation starship.
So Sisko knows that he is not targeting Maquis combatants in general or even the specific combatants who attacked the
Malinche.
Furthermore, Sisko's own words show that he knew what he was doing was wrong. In his conversation with Jadzia when he comes up with his plan, he says "it's time for me to become the villain." He later admits that he did not inform Starfleet of his plan and says that taking a big gamble is "what it takes to be a good villain."