I came across this a couple of years ago when I was asked for a signature for the reburial of the bones found at Avebury, West Kennet Longbarrow I think. My first response was what about all the other bones that are found through the years in town sites, the reburial aspect becomes enormous, so was left with the feeling that you could'nt discriminate for a particular set of human bones whether pagan saxon/christian or prehistoric, but that you should at least treat all bones with some respect but that reburial in the same place was a knotty problem and not always possible.
Sebastian Payne chief scientist at EH is I believe also a pagan and probably has the best views on it... an article from 2007 gives his interpretation of how we should treat the bones of the dead...
http://news.bbc.co.uk/1/hi/england/wiltshire/6385675.stm