Apparently you're ignoring the part where the colonists were intended to be relocated and -at their request- were given the -option- of staying where they were under Cardassian rule.
Now forgive me, since I don't have all the details on the treaty, so I am basing this on personal opinion from what I saw during my viewings of DS9.
If the treaty was signed before discussing the issue with the various colonies, the Federation government screwed up, royally. It's one thing to convince people to leave for the greater good, it's quite another to give them no choice or input. So yes, the Federation certainly intended to relocate them, but I never got the impression that the colonies had any say in the process at all, which, as you can imagine, would upset all of those colonists who saw their worlds as their new home that they built.
On the other hand, the colonists took a gamble, and bet that if they stayed, the Federation would not allow its citizens to be unjustly treated by Cardassia, an aggressive, fascist state, much like Western governments wouldn't exactly stand to see their citizens being unjustly treated when visiting nations like China. In the end, they were still Federation citizens, even if they were now apart of Cardassian territory, and they should still have the rights and freedoms of all other Federation citizens, no matter what world they live on, or the amount of political influence they can leverage
The Federation was protecting its people by signing the treaty. Specifically they were protecting millions of people from a war with Cardassia. Treaties -always- involve compromise. It's the way the universe works, and yeah, it sucks if you end up on the short end of the stick, but if you'd really rather have a war between two powers than move? That, IMO, doesn't speak well of you.
Compromise can be achieved without infringing on the rights of your citizens in such an unjust way. These colonists had the protection of the Federation...up until the Federation decided to wholly cede colonies without their input. Imagine any democratic state ceding territory in such a way to a fascist dictatorship.
Hell, let's imagine the United States ceding Maine to Canada without the input of anybody within Maine. Once the treaty is signed, they're told to relocate. Yeah...I don't see that playing well, and that's from one democratic state to another.
We have no idea exactly what the Feds may have done once they became aware of what the Cardassians were doing. Sisko's team made a point of trying to stop the Cardassian arms shipments, but "The Maquis" doesn't make it clear what other repercussions may have ensued.
Sure we have an idea. There were none. The Federation didn't carry out anything within the series against Cardassia over violating the treaty by arming its colonies. The Federation did not do anything to protect its citizens from Cardassian violence. The Federations did not make the Cardassians abide by the treaty, and abandoned its citizens because it might start a war...
Oh, but wait, once the Maquis started fighting Cardassia, the Federation was more than happy to fight the Maquis. Sisko freaking gassed a Maquis colony without any canon consequences.
Oh, and should we forget how Cardassia basically kidnapped O'Brien from Federation space and framed him as a Maquis agent? Seriously, compromise in treaties are fine...if both sides are acting in good faith. As we're all aware, the Cardassians weren't.
To be honest, how the Federation handled the Maquis on screen, I'm amazed that huge swaths of non-core worlds didn't rebel immediately. How would you feel if you lived near the Romulan or Klingon border, (just to name two) and realized that, if the Federation decided it was necessary, will sign your home away, and will not protect your rights even when it blatantly violates the treaty they just signed. More than that, if you try to fight back, they'll help said treaty violaters against you, and if they're having a really hard time with one of your rebellion leaders, might just decide to use a WMD against your colony without any consequence.