Sisko's actions weren't on the same level as Eddington's.
Eddington, by the very action of initiating
the use of bioweapons, demonstrated his belief in his own ego (and possibly the genocide of the Cardassian race). Eddington would have been quite happy to kill every Cardassian in the DMZ, whether or not they were involved in any actions against the Maquis colonies.
Sisko, OTOH, simply leveled the playing field. By deploying the same weapons against the Maquis, Sisko merely ensured that the two sides - Cardassian and Maquis - would have to exchange colony sites. Nothing more than that. By his own actions Sisko stopped any further genocide, by ensuring that the Maquis would have to give up no more, and no less, than what the Cardassians would have suffered at Eddington's hand.
Side note: If Eddington had lived to see what happened to Cardassia itself at the end of the Dominion War, I wonder what he'd think. He'd probably be laughing his ass off.
Oh well...whether it be a personal comparison (Sisko vs. Eddington), or Federation vs. Maquis, the basic theme is the same. Order (Federation) vs. Chaos (Maquis). The same process repeats on multiple levels.