I would prefer one shrine per religion per region.
But one per estate could work. Though what would happen when estates are removed by the lord?
If it was one per region that would make this more of a lord level decision, which would defeat the purpose as lords can already build temples and the goal was to add more to the "knight game".
I'd say if the estate is destroyed the shrine is just no longer tied to the estate. It becomes no different than a shrine that a priest built.
