This is very interesting. It's understandable that the OS would assert their copyright on map reproduction, but I find it difficult to believe that the NT has any reasonable cause for complaint. I'm not an expert on copyright, and it's a notoriously complex area, but I don't think ownership of an artifact transfers copyright to the owner. If this were the case, an art gallery would own copyright to all the works in its possession, and a person buying a CD would own the rights to its reproduction.

This leads me to question whether the NT have a case. They may 'own' the sites, but surely the photographer owns the copyright for their photographs. If you take pictures on land owned by an authority but freely accessible to the general public, I don't see how that authority could assert control over your work - assuming that the work is completely benign. (Private land may be a different matter, I don't know).

It might be worth speaking to someone who's published archaeological work in the past. Maybe a local university department? A publisher?