I helped the NCR take back their prison and finished the quest but when I check on the map, I am still vilified by the prison. Glitch or did I miss something? I want the NCR to really take over it again.

The NCR never really take it over, they just sit inside.

The building is associated with the Powder Gangers so it displays their reputation level.

Thats stupid. It belonged to them in the first place.