Wasn't Starfleet also playing very gently at first, not wanting to appear like another invasive power after the Cardassians withdrew from Bajor? The station was Bajoran property, with Starfleet administering it, and them providing a liaison officer from the Bajoran military per the provincial government.
Yes exactly. It wouldn't have made sense to assign an Admiral or other senior officier - that would have been inflammatory in a delicate situation and increased the perception that Starfleet was simply replacing the Cardassians as the overlords of Bajor.
The initial assignment is pretty modest - he's there to coordinate relief efforts to help get the planet back on its feet, at the same time showing the flag and influencing the Provisional Government towards Federation membership.
The Starfleet higher ups may have assumed the same as Kira and Quark - the government would soon fall and lead to civil war. Sisko had apparently just rolled off the shuttered Defiant project so was available and had the right skills. He had the right character too, he was a builder by nature and not one to throw his weight around and let his ego take over.
Once he's there, he's unassailable because of his unique status as Emissary, but Starfleet keep him on a pretty tight leash. We see various Admirals over him, particularly regarding the Maquis and the Cardassians.
It's interesting that he isn't replaced during his leave of absence, or at the end of the series. Kira takes over and is trusted to do so by Starfleet, and Bajor by now has a stable government and a mature relationship with the Federation.
Shadows and Symbols shows that Admiral Ross is still looking out for Starfleet's interests, but he can't directly order Kira to do something as long as she retains the support of her government.