Well the Maquis were eventually planning to become a separatist force, after they got rid of the Cardassians in the DMZ, they were planning on declaring those colonies in the DMZ a independent nation. I'm not sure what the Federation could have done to stop them.
I think the best way to answer this question is to ask what would happen if the government of one of the German lšnder
, provinces of Canada
, or states of Australia
, were to be taken over by a dictator like that. They're all federations, after all. Would the Federal Republic of Germany, Canada, or Commonwealth of Australia tolerate such a state of affairs?
Well the province of Quebec has held two referendums on whether to become a sovereign nation, so there have been seperatists movments in one of the countries you mentioned.
Also a colony or a Federation world need not become a dictatorship to have values that oppose the Federation's. The Maquis' ultimate plan was to have the colonies in the DMZ separate from the Federation, because they felt the Federation has failed to protect them. Would Eddington had been a dictator or started a democratic government in this new nation? We may never know.