Golf as a popular sport is fairly young, about as old as American football, perhaps a little younger. Golf architecture is a very new discipline as compared to the other arts. Prior to 1900, most golf courses were very crude and primitive. I can't imagine why or who would have wanted to preserve these courses. In fact the birth of golf architecture as a professional field was in reponse to the bad work. Many of these old links that we now consider the ancient work of guys like Old Tom Morris in most cases actually owe their current state to those first golf architects - guys like Colt, Fowler, Simpson etc. After 100 years of golf architecture, it seems reasonable to me that we start recognizing, preserving and protecting the game's most important designs/courses.
I'm not sure courses that are very well-preserved should be the determing criteria, some courses have evolved over time and are currently at their zenith - for example Rich's Dornock which dominates his very narrow perspective.
I would suggest there be far more than a dozen courses worthy of designation. But I would also create a number of different disignations - Landmark designs for the GCGC and NGLA type courses; a designation for greatest works of the master architects - Camargo, The Golf Club, Seminole, Shinnecock, Hirono, Jasper Park, etc; a designation for courses that have evolved over time - TOC, Dornoch, Ashdown Forest, Woking, The Country Club, Ballybunion; a designation for courses that were landmarks or master works at one time but are now in a state of distress or altered for the worst - Yale, Timber Point, Riviera, Bel-Air, ANGC, etc. (perhaps acting as an incentive to get their act together). And I'm sure there are other posibilities/criteria that should be considered.
Obviously you can not force a private club to preserve/protect their golf course, but this elite recognition would hopefully be a point of great pride. As a side benfit it could act as a tool to educate the membership of these clubs, to explain what they have (had) from architectural view and why their course is so important from an architectural perspective. I would also suggest that when a course that has been recognized contemplates a change, that those changes, and the indiviuals carrying them out, be closely scrutinized by the same organization - don't you think Merion would have benfited from such advice?