1000 of those came his freshman year. He was used much, much differently after that. His senior year he averaged 2 ypc.
That doesn't make him anymore of a statue. He still has the ability to run and elongate plays, but instead of just heading straight up the field they are asking you to take one more look down the field for a receiver. Yeah his role changed, but he is still not a pocket passer. It is like when the great Pinkel tried making Brad Smith into a pocket passer. His rushing yards fell, but it didn't stop him from still being a threat. The next year they let Smith go back to what he did best and his rushing yards escalated again. If it is in your arsenal, you have the ability to use it and that is what matters.