The Bajorans were leery enough of what little Starfleet presence was there. The feddies only sent a Commander because a higher-ranked officer might have signaled a new occupation to some of the Bajorans, specifically the jumpy Resistance guys. An Admiral or Captain signifies a permanent presence (and an Admiral a significant one), but a Commander shows enough rank to get things done, while still signifying a temporary/joint command.
I agree with this. Eventually, the Bajorans were probably going to want to take over their own territory when they were ready. That looked to be a bit of a ways off (many years, really), but they got the right balance having a Commander there who became even more than that to them, a Captain and an Emissary.