I just re-watched The Maquis, so I have one important part of the puzzle: crushing the Maquis risked war with the Federation. Or, more accurately, it would involve breaking a treaty which had been very favorable
to Cardassia. Compared to what they gained through the treaty, the damage the Maquis did was tolerable.
The Maquis used the Badlands to their advantage, certainly, but the main geography working in their favor was the DMZ
, a large area that the Federation and Cardassia had mutually agreed to keep military forces out of. Cardassia could not just go in and crush the Maquis, because sending warships into that area would break the treaty. If they found a Maquis base, they could tell the Federation and negotiate going in to destroy it, but by the time they did all that, it was gone, having moved to some other planet.
Once the Dominion entered the picture, the Cardassians no longer needed the treaty with the Federation to keep what they had, so they broke the treaty and sent in the warfleets and killed the Maquis pretty quickly.