No, Coach K's reputation is fine, and I think it always will be. I could see him perhaps suffering some burnout after the Olympic games, but being tired doesn't sully a reputation built on decades of excellence. Because he has mostly stayed away from the "one-and-done" type of player, perhaps it might look as if he doesn't recruit as vigorously as he used to, but I believe that is a conscious decision on his part in an effort to build consistently good programs. (And, of course, I am guessing here--I have no insight into his methods or intentions..)
Coach K might not be the best coach ever (although he certainly has a chance to be the winningest coach ever), but he will always be regarded as a great coach and one of the best in the history of the game.