Hope the cold is soon a thing of the past, LS!
Without repeating the "Circles under churches" thread, it might be useful if we compiled a list of sites where church and megalith are in close juxta-positon. We might have three lists - one of definite co-existance like Rudston and Knowlton, another of close association - Avebury and Stanton Drew and then the third where a church has been built using the fabric of an earlier secular building such as Bradwell-juxta-mare in Essex.
Then we could compare the tiny number of sites on these lists with the enormous number of megalithic sites which are NOT associated with churches.
Beware of false clues though - there is a megalithic slab in the churchyard at Winterbourne Monkton. However it was robbed from a nearby barrow to bury a local vicar! That church was not built because the megalith was there first. http://www.megalithic.co.uk/modules.php?op=modload&name=a312&file=index&do=showpic&pid=8522
I can certainly see the desire to believe that Christianity incorporated pagan circles and stones in their churches in order to subjugate the "old religion" The veneration of trees, stones and springs continued and there are specific written records to prove it - there are specific written prohibitions and punishments. However, ask yourself if there is any evidence that Neolithic stones and circles were used for religious purposes at the time of the introduction of Christianity? Is there even any evidence that they were still being used for ritual in the Iron Age? The Romans had their pagan and Mithraic temples, some may have been churchified. Roman writers tell us that the Druids preferred groves to temples, the Germanic tribes also preferred the open air.
Rhiannon is right I feel - the Anglo-Saxons and medieval society largely ignored the stones and found them to be a nuisance and obstacle to the plough. A few were said to be the work of giants or of Woden, but the rest were simply ignored or used as a source of building materials.