Borders have been redrawn for centuries on Earth, and yes sometimes a group of people are affected by it.
So place yourself as the Federation President, would you not sign a treaty and risk a war that could potnetially cost tens of thousands of lives or a agree to a few worlds swapping ownershp and relocating those citizens.
Which is more important those worlds of the lives of thousands?
I think many would say preserving life is more important. Remember the Federation wasn't abandoning these people it offered them relocation.
If I was Federation president, after the Cardassians destroyed the Federation colony in "Ensign Ro" and tried to put it on the Bajorians, I'd be skeptical and any treaty I enter into would take that sketpicism into account to say nothing of repirations for that slaughter.
Suppose I decided to give them a second chance, that was just during the armistice after all, so while my representives are trying to finalize the peace treaty in "Chain of Command" they then try and sieze Minos Korva to dictate favorable terms. I think I'd start to get the idea the Cardassian Union isn't at all interested in peace.
Even after the peace treaty was signed, the Cardassian time and again would attack Federation targets whenever there was an advantage to be had. TNG's "The Chase" and DS9's "Emissary" are perfect examples.
By the time the Maquis even became a concern, the Cardassians had a clear pattern of aggressive behavior, treaty or not. If the Federation was too chickenshit to stand up to a technologically inferior fascist power that was into hostile expansion at any given oppurtunity, I wouldn't blame the colonists one bit for standing up for themselves.