It seems to me that the argument for holy wells being prehistoric sites could equally apply to churches.
They both:
Are Christianised sites
Are usually named after Christian saints
Usually have a stone structure built in Christian times
May have been used previously by non-Christians
There's usually no visible or written evidence of any use prior to Christianity.
Here's one of the churches on here which I don't think belongs:
http://www.themodernantiquarian.com/site/4529
The presence of sarsens in the vicinity indicates to me that the stone wasn't used, if they had of been used then they wouldn't be merely sarsens.