I need to check more carefully but I think the 'Waden' of Waden Hill means Woden Hill, while the 'Wee' of Weedon is the Old English weoh - the same word which I think gives rise to the word 'Welsh' (the Anglo-Saxon term for a foreigner or, in this case, a savage). In other words, and based on the etymology, Weedon Hill seems to suggest a hill with a 'Welsh' temple.

The relevant bit from Stukeley, and the drawing which Pete has noted elsewhere, can be seen here at http://www.avebury-web.co.uk/silbaby.html (halfway down).