It would probably quite easy to protect these sites from damage from trawling. All you have to do is drop a number of large jagged, heavy objects on the seabed on the margins of the area e.g. wrecks. No skipper would risk fouling his nets over ground like that. The area could still be fished, just not as intensively, which is better for preserving not only the archaeology but also the local wildlife. Double bouble!