Why destroy the station in the first place?
For the same reasons the original Enterprise
and the Enterprise
-D were destroyed--to do something shocking that forever changes the status quo.
Besides didn't they tow Empok Nor into the Bajor System (it was a DS9/SCE crossover)? Couldn't they have just activated it and had it become Deep Space 9-A?
I think in-universe, Starfleet may have decided to build a new state-of-the-art starbase that met Federation specifications and requirements rather than try to repurpose another abandoned Cardassian ore facility.