The progression seems reasonable to me when you factor in the pardon the Maquis got - after rejoining Starfleet in the merger of the militia, she now had several of Starfleet's most decorated figures, at the least Picard, Kira, and Vaughn, in her corner and saying that they trust her with great responsibilities. Given DS9's strategic importance over the years, Starfleet is probably also more prone to promoting within the ranks of the station's crew to keep the well-oiled machine functioning, rather than sending in a new CO who has little familiarity with the day to day workings of the station.