have been difficult to do anything about the menace without systematically killing or imprisoning everybody in the DMZ - because anybody could be Maquis, or become Maquis. Confiscating of weapons would also have been an immense effort, because handguns in Trek are by no means rare or difficult to obtain, and an individual Trek handgun may amount to an artillery piece when used correctly.
The one possible way to stop the Maquis would have been suggested by "Ensign Ro" already: deprive everybody in the DMZ of interstellar transportation. Spacecraft, while common, would still be in shorter supply than guerillas or disruptor rifles. And it might be possible to confiscate every spacecraft and still appear halfway humane to the rest of the galaxy. However, something like that was no doubt explicitly forbidden in the DMZ treaty, because the very idea of that treaty was to allow the colonies in the Zone to continue to eke out a living. And the UFP idea of a living would no doubt involve interstellar travel, as the Feds wouldn't consider the colonies self-sufficient even if by Cardassian standards an isolated colony might still be a viable place to live in.
Once the treaty was out of the way, though, it should have been an easy thing to confiscate or destroy 95% of the spacecraft in the area, and to let the remaining 5% that were hiding in various Maquis holes to fight the futile fight and quickly perish. No need to massacre the population or anything - although the Dominion or the Cardassians might also have gone for that just for the hell of it.