I've just been reading Pollard and Gillings' 'Avebury' (2004) and I think they're implying that in Saxon and early medieval times the circle seems to have been pretty much ignored. That is, it was just seen as some ancient old earthworks, not sacred, not a pagan threat, just a bit of landscape history. When it was mentioned in the Domesday book (the first written evidence we have) it says 'Rainbald the priest holds the church of Avreberie to which belongs 2 hides. It is worth 40s." as though the henge wasn't even worth mentioning. Even when it was called 'Waledich' it implies just a ditch like a hillfort, not anything spooky or magical.
(P and G have an interesting discussion of the 'stone burial /destruction' issue as well.)
Besides, on the subject of churches - surely you could say the same (that there's a high density) about any number of places - most tiny villages in England have a church. If you go to Norwich you can't turn down a street without tripping over one.
And you're bound to use whatever stone there is to hand so if there are big sarsens just begging to be used, you'd use them would you not? They were just hanging about in the fields. I don't see that sticking them in the foundations implies any notion of putting paganism in its place, necessarily. One wouldn't make that conclusion in places other than Avebury?
(just a few thoughts)