Leaving aside my overt prejudice against Christianity for stomping on Paganism, I see no problem with actual prehistoric elements of a church or churchyard being listed on the MA. Julian did it himself in the book with [[Ysbytty Cynfyn]].
The problem with listing churches where the evidence of prehistoric activity is gone, is that all you can look at is the church itself. I know of quite a few empty fields that once had megaliths in them. I could post those up on the same grounds.
Sorry to be negative, but personally I think churches are a bit off topic (along with fogoues, brochs, castles, Celtic crosses & inscribed stone, and tenuously proven sacred hills).
Kammer x
PS. Those Geocachers have put me in a pissy mood. Sorry.