Except the Maquis -were not- the Federation's own people. They not only made a point of renouncing their citizenship, but then Eddington specifically began attacking Starfleet vessels and critically disabling two.
I believe Sisko himself says that the Maquis had escalated matters to the point where they were now considered a threat to the security of the Federation.
Do we have any reason to believe the people huddled in caves were -not- Maquis terrorists, especially given that Sisko was in the middle of being lured into a trap at the time?
What would you have had Starfleet do in order to capture Eddington before he could poison additional planets? Use harsh language?
Hell, I'd say Eddington was the Maquis' own worst enemy, because if they'd kept their tactics low-key then Starfleet might have let things slide for awhile, but the actions he engaged in escalated to the point that they could no longer afford to ignore him.