From what I heard, the church came about because an old graveyard had filled up, been abandoned, and later scheduled for development. So they had (literally) tons of bones they needed to dispose of. And nobody would take all that calcium phosphate.
Not even ground up as fertilizer.
Then somebody had a bright idea. Why not use the bones as building material? And what better than a church built out of bones? Be a constant reminder of those who came before, and who have passed on to God's Kingdom.
Also serves as a reminder of our transience.