I've watched lots of DS9, actually. But it has been a while. And there's probably room to dispute whether some of the Maquis targets were really civilian. If the freighters were carrying weapons sent by the Central Command, are they a legitimate military target, even if civilians are running the ships? I'd not put it past the Cardassians to disguise their own soldiers as civilians to ship weapons to their own colonists. It's something they'd do.
terrorism? Is it something that only happens to civilians? If so, blowing up freighters would be, I suppose. But what if the civilians are contracting with the government? Is it a legitimate target then?