The Bajorans put up with the station when it served their interests but it was always a reminder of the occupation.
Maybe at first. But it was also a major installation owned by the Bajoran government and essential to putting Bajor on the map. Plus it gave their system a unique identity even after they joined the Federation. I'd propose that the station became just as much representative of free Bajor as it did the occupation. If so, I could easily see the Federation being sensitive to the Bajoran sense of national identity and weighing that into their decision regarding the new station's design.