On the other hand, if it's displayed in a museum with suitable preservation techniques there's a chance that more of the people it belongs to will get to see it. I would have thought that wood in a wet environment with wind and tides would be bound to deteriorate eventually, so this seems a longer term option.
I agree that the location is important but the situation isn't really comparable to Stonehenge, given the different materials, and it must have been a difficult call. Francis Pryor said on camera that he would pay more attention to the views of others, eg new agers, in future, so perhaps his mind is opening just a bit. Don't forget, though, it's the academics who have revealed oodles about our past and who seek in their various ways to preserve it for our future.