I believe in "For the Uniform" Sisko specifically states (sorry!) that because of the Maquis' actions in attacking the Malinche they've become a threat to Federation security and as a group are no longer considered civilians for these purposes.
That said, how much of it is Federation-sanctioned and how much is Sisko being a badass isn't made clear.
He had absolutely no authority to chase Eddington, as was stated earlier when the captain of the Malinche
basically told Sisko that he was taking over the hunt, and to back off. However, this is par the course for Star Trek shows, so, that'd be forgivable (like when they went to rescue Odo in The Die is Cast
) although he'd probably get a browbeating for disobeying orders.
However, he freaking gassed a colony. He had absolutely no authority to do so. Look at how uncomfortable his OWN CREW was at the order, how do you think the various dispassionate Admirals would react to Sisko proposing gassing Maquis colonies because ONE SHIP was disabled. It's too bad they didn't actually relieve him of command, would have been much more interesting, and highly justified.
More importantly, as Eddington rightfully stated, that colony had nothing to do with the Malinche
. At all. But, going with Sisko's argument, any town sympathetic to the Taliban in Afghanistan can have nerve gassed dropped on them.
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. When you attacked the Malinche you proved one thing, that the Maquis have become an intolerable threat to the security of the Federation, and I am going intend to eliminate that threat.
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.
I like Sisko, I really do, but this episode is quite possibly where I could see him as being the bad guy. He had more guilt over one pro-Dominion Romulan senator over gassing a colony of hundreds of thousands of people.