Technically speaking the Maquis are a Cardassian problem, as they should be on the colonies on the Cardassian side of the border.
He had orders from Starfleet to deal with the problem, and the method used was well within the laws and traditions of the Klingon Empire. As far as the Klingons are concerned, the action is legal and binding. Even Worf's passing over the leadership.
You know, it might be murky whether or not The Sisko committed a crime stopping Eddington, but there are other things he could potentially hang for, like ordering the death of Head of State of an Ally. How come no one ever brings that up?
He had orders from Starfleet to deal with the problem, and the method used was well within the laws and traditions of the Klingon Empire. As far as the Klingons are concerned, the action is legal and binding. Even Worf's passing over the leadership.