Can't see any reason why the stones shouldn't be re-erected - they were only downed a few hundred years ago and it's not like we're trying to protect an 'evolved' landscape.
As so often it's probably a question of finance (how much does it actually cost to raise one stone?). Guess it's pretty expensive so suggest NT start a 'Raise a Stone' Campaign. What the hell, even if there's a little blue plaque next to each stone for five years reading 'This stone was re-erected with the help of generous contributions from the Marlborough Masons (or the Pagan Federation or the Modern Antiquarians etc etc) so what? The plaques are there for five years - the stones are there forever.