Eddington was taking advantage of the chaos in the cardassian empire and pressing his advantage. He was probably within months of driving the Cardassians from the DMZ and declaring an independent Maquis state.And... Eddington was already running around poisoning planetary atmospheres and killing a lot more innocent people. Sisko tried other means for Eddington to stand down and Eddington just laughed. What's he supposed to do, take the Arnold Rimmer course in warfare (wearing glasses, wearing t-shirts that say "Give quiche a chance", and coming up with groups such as "The Committee for the Liberation and Integration of Terrifying Organisms and their Rehabilitation Into Society"?)
"At what point do conventional means fail" is one of the issues of the story and it was spelled out.
He was forced to attack Federation targets because the Federation intervened.
Disclaimer: I am an Eddington fan.