Massive topic, Littlestone and I'm not sure if this is the right place to talk about Dark Age communities, settlements etc.. I'm only too willing if the eds permit.
One quick point relating to the Avebury stones - the earliest Saxons built in wood and had no tradition of building in stone. Later Saxon churches were built with stone and recycled Roman bricks and tiles. It is generally agreed that the first Saxon settlers avoided Roman sites (just like TMA ;o)) and built some distance away. So that may have been the case at Avebury. They came, saw the stones in what they took to be a fort or walled ditch (Afa's burgh or Waleditch) and simply built thir wooden houses and church nearby thus avoiding the haunted stones.
One little gem for you - apparently the little chapel of St Non at St Davids in Pembrokeshire was built during the 6th century INSIDE a stone circle. (St Non was St David's mum)