I don't know if it is possible to replace this monastery for rebuild with a monastery for use. Maybe it is, in one campaign mission I think that the player needed to achieve something, and after that, before moving on with the mission, some changes to the map were made. Such as part of the forest clearing up. Again, maybe I'm wrong... But I've been seeing these things, such as changing ownership of a castle, making some castle lord your ally, etc. I only can't tell if I saw some of those things in the campaign, or in custom scenarios as well. Simply, there are some stuff that the guys from Firefly made in the campaign, which we simply cannot do in the editor.
But there would be some workaround... You should be able to reward the player for repairing the monastery with the needed knowledge to make a monastery of his own! So at start the player wouldn't be able to build the monastery, and after that they would. I think you could do it by making missions. The first mission would include rebuilding monastery, and in the second mission the player would be able to build a monastery for themselves.
I think this would make sense in either way, whether the players can build a monastery in their original estate, or the player's estate changes in mission 2, and not the player can build a new monastery in their new estate... Just some ideas, but I'm not very experienced in this as you can guess.
At least not as many other scenario makers.