I've seen several circiumstances around the country where large stones seem to have been incorporated into the fabric of a church in this way.
I'd urge caution in giving them a 'pre-church' pagan providence.
I came upon some such yesterday in Hertfordshire. St Mary's, Pirton has large stones underpinning several of the buttresses on the outside of the church, similar to those used in Pewsey, and also in Amersham (where the stones are largely puddingstone). See http://i27.photobucket.com/albums/c194/ocifant/IMG_4628.jpg for an example.
In this case, reading the church history booklet solves the mystery, where it states that the stones are the remains of a previous church on the site, dated in the 15th century, and marked as such on the church plan. That isn't to say that all such stones have a similar origin, but it's worth popping a quid or two in the box to have a squint at the church history booklets for any clues...
