No other sarsens nearby? Look in the farmyard opposite the church, look in the garden of the large house - they have a sarsens folly. Unless we have been to two different places, then the sarsens are everywhere. The neighbouring (and older) church at Alton Barnes has massive sarsen stones forming its quoins - they are enormous and totally megalithic in character. Now that may well be worth a closer look!
I'm not adverse to accepting that the church could have been built on a pagan site. I have already quoted the Papal edict that pagan temples were to be reconsecrated, but the idols of stone and wood destroyed. However, I believe that the churches replaced pagan SAXON sites and not prehistoric ones unless in specific cases it can be shown that the Saxons had their temples or groves on such sites. In some cases they clearly did eg the conversion of earlier round barrows into moot hills and their intrusion burials into both round and long barrows.
Some evidence of pre-Christian useage at Alton Priors will happily convince me. As for the trapdoor, well you know that the old time antiquarians were often vicars. They were romantics too and loved to fantasise about Druidic rites and all that. So following floor repair, what could be more natural than to keep open access to impress other gentlemen scholars ;> )
