Basically we are not too far apart and I would go along with the idea of different circumstances applying in different places. Perhaps the church became more intolerant as it grew more powerful.

Having said that, we do have to look at the dates of the buildings where these stones are now found - albeit there were probably earlier churches on the same site. I find it easier to accept the idea of pagan stones being assimilated into the earliest churches in order to win over the locals. But when churches date from the 12th-16th centuries it seems much more likely that the stones would just be seen as stones.

Puddingstone and sarsens are very hard indeed and difficult to dress (puddingstone is almost impossible). So then it seems much more reasonable to see them used as part of the footings, unless there was residual paganism locally and then they would be "put down" rather than honoured or venerated. The gods of the old are the demons of the new.