The remains were almost burned up:
http://news.bbc.co.uk/1/hi/sci/tech/604067.stm
The claim is that it certainly wouldn't have lasted another 4,000 years:
http://www.northcoastal.freeserve.co.uk/seahenge_assessment.htm
The parts that remain buried are fairly well protected. But, every time it's uncovered, it gets scoured by sand, eaten by critters, etc. The contention is that the peat that formerly protected it from erosion has been washed away, leaving it to the mercy of sand. I've no way of assessing that claim. But, in pictures of it, you can see that the posts are worn down to or below the level of the central stump. Surely it wasn't built with short little posts no taller than the central stump?
That locals had seen it uncovered before is kind of beside the point. Had any of them been keeping any precise record of its condition; monitoring its (alleged) rate of erosion? Of course, a program of monitoring could have been instituted. And in the meantime, how many vandals and souvenir seekers would have been hacking or chipping at it? If the discovery could have been kept secret, that might have been an option. (Many, if not most, archaeologists in our American Southwest no longer publish the location of Native American sites at all, for fear of looting.)
To me, given that the setting is not today what it was when the thing was built, protecting the bits is more important than taking the chance it would be further damaged. Of course, with news like that cited above, one wonders how much protection they'll receive.