It was probably a matter of who got there first. Wutteat, Consult, The Dunyain, and Kellhus all had reason to blow it up. Lots of plausible theories, but who got the prize? I'd say Wutteat got there too late, so I rule him out simply because of the timeline. As for the other three, I can't decide. The Consult had a long time to look, The Dunyain may have realized something was wrong, and Kellhus could have done it before he liberated Shimeh or at any point after.
Last few posts should probably be moved to Who Destroyed the Dunyain Monastery.