As previously mentioned, Leyton claimed that he had moved things behind the scenes in those two episodes he was in. Really, Sisko seemed to be on the proverbial backburner. He had already served as an Xo on at least two different ships, then after Wolf 359 seemed to be wasting away with the Defiant project.
While not ready for a ship of his own, seemingly disgruntled in Starfleet, what else are you going to do with him? Telling him to be XO on a 3rd ship would just be a blantant "you're not ready to command" and probably run him out of Starfleet for good. Leaving him in R&D would probably be a waste of all the command, tactical and leadership training they had to have given him. So sending him to a small, obscure outpost to command, which was what Bajor was given there were maybe a 100 Starfleet personel there and the rest were Bajorians, was pretty much all they could do with him.