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.
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.