The Maquis should have left the colonies. It's the 24th century in Trek, re-settling elsewhere in the Federation should be easy.
You do realize that we are talking about multiple planets with no idea how many people are actually living there so moving them could require a large amount of ships which have to come from somewhere (hell it took Picard a few weeks to just get evacuation ships to move a small colony descended from crash survivors so who knows how long bigger colonies would take), then there is the question of where to put all the refugees I mean it not like the federation has an infinite amount of planets hence why the planets being ceded were colonized in the first place, (again Picard and his crew spent time looking for a new planet for the guys from Homeward so it's not exactly a cake walk). Which is another problem with the treaty.
Seriously when do people not realize that a planetary evacuation isn't some minor project and is in fact a major undertaking. It's a freaking planet not a small town.