Meanwhile the Maquis disenfranchised themselves, and the Federation said "Go #### yourself" you are too still Federation Citizens who have earnt yourselves a billet in a Federation pokey.
No, it wasn't that simple.
At that point in time, Klingon/Federation relations were strained to say the least. The Klingons were getting VERY chippy at that point. Worf and Picard got pretty deep into the Klingon politics, which made the Klingons even less happy with the Federation, as many of the Klingon High Council were holding very personal grudges. War with the Klingons was a distinct possibility.
The Romulans were being very Romulan, with the Tal'Shiar taking more and more direct control of government operations. Not to mention Empress Sela with a very personal grudge against the Federation.
The Borg had strolled in, not too long before, and cut a huge swath through the Federation fleet, and no one knew when they would return.
So the Federation is on the verge of outright war with the Klingons and the Romulans, while at the same time being in a much weaker military position due to the losses to the Borg. The ships lost were a big hit, but the tens of thousands of trained, dedicated officers lost was an even bigger hit. Ships are much easier to replace.
While ALL of this is going on, the Cardassians start getting more aggressive, and made it clear that they considered the colonists and the Maquis as Federation members, and that if the Federation didn't actively do something about the Maquis they would hold the Federation responsible for the Maquis' actions.
The Federation was backed against a wall. Failing to act against the Maquis would have resulted in a war with the Cardassian Union. A war with the Cardassian Union would have resulted in the Klingons AND the Romulans using that as an opportunity to apply even more pressure to the Federation. Klingons attacking directly and Romulans... being Romulans.
Weakened and battered, a war with just one of those groups may not have been winnable, and there was no chance it would have stayed a war with just one of them. The entire Federation would have fallen, with the burning remnants divided between the Klinks, Rommies, and Spoon Heads.
The needs of the many outweighed the needs of the few.