Unfortunately diving the Thistlegorm is and remains one the messiest dives to undertake - especially if you are a diveguide. If, on top of that the guide or the boatcrew (or both) are inexperienced or don't really know what they are doing, disaster can strike.
I don't think mooring buoys would be a feasible concept here, as the position of the boats are mostly dictated by weather/sea conditions. During high season one can count as many as twenty boats on the wreck, so that would be a lot of buoys, considering that most boats use one anchor plus two lines tied to the wreck. Setting a dozen or so moorings would limit the number of boats present on the wreck (certainly good for the wreck and the divers) which in turn could cause either outrage or ignorance from the dive operations. In the latter case more boats will hook up to one mooring and cause them to break - back to square one.
Liveaboards actually have moorings - ropes are tied to the Thistlegorms anchor - but still they need to tie up to the bow of the wreck, if only to have a descent line for the divers.
Of course there has been damage to the wreck from various sources (divers, guides, natural deterioration) but IMHO the worst factor are those diveguides that will tie their lines to virtually anything, risking not only to damage the wreck but also their own boat as well as others.
One solution could be to actually limit the number of boats/divers allowed on the wreck per day. On the other hand, this would damage the dive operations and I seriously doubt that the egyptians could pull a thing like that.