If it is consecrated ground then there is likely to be strict covenants and such attached to it. If it's a public graveyard with remains still buried then that could cause a number of potential issues. The land the church is on may also have restrictions.
When thinking why mortgage lenders have these kinds of criteria, essentially if they end up having to repossess they want to be able to sell the properly quickly for the best price possible without a complicated sale.
If you proceed I'd find an experienced property lawyer, preferably one who has dealt with this kind of land and finance on this kind of land previously.