Sisko asked Quark just before he left to remain where he was since the Cardassian occupation so there was some life on the promenade.
> The dirty secret is that Starfleet is actually a totalitarian military dictatorship, on the ground and in the air. That's how they got to take over the Palace of Fine Arts.
Starfleet is a paramilitary organization and Deep Space 9 is a military installation under their control (it has sufficient firepower to defend itself against many of the strongest warships), just like the starships - that's no secret nor is it dirty. There can be civilian elements on military bases. IRL there are civilians living within military areas in some countries - governed/commanded by the military.
But SF doesn't control the Federation, nor Earth or other civilian settlements. There is an episode where Sisko and Odo thwart the attempt of a rogue Starfleet admiral to get Earth under SF/his control.