Sisko had every right to go after the Maquis for attacking the Malinche
. An attack on any Starfleet vessel is an attack on all Starfleet. The Maquis attacked one ship, they can do it again. It's Sisko's responsibility to come to the aid of his fellow captain.
Sisko was entirely correct. By that one attack, the Maquis proved their hostile intentions towards the entire Federation. Sisko would be remiss if he did NOT go after them for it.
And perhaps if Eddington enjoyed manipulating Sisko so much, let's see how he likes BEING manipulated for once.
Also: for the thousandth fucking time, all Sisko did in his attacks was force the Maquis and the Cardassians to exchange colonies. No one was left homeless, no one died. If Eddington had gone unchecked, though, there'd have been casualties aplenty...