Currently there is no way to remove relics once they are inside a building. Ive put a relic in a tower for example and there is no way to get it out again. The only way to do it is to delete the building itself.
If I remeber correctly, you can retrieve them using a monk. Right click on the building with the monk selected and he should go and get a relic.
Havent thought of that, thanks it works indeed.