I haven't been watching McCoy's games or stats, but remember that Smith did most of his work in three quarters, and was then replaced by Zwick or Boeckman. He rarely played all four quarters, I think against just Texas and Michigan. He could have easily run his numbers up if he had remained in at quarterback for the full game those other times.
Yes, and comparisons based on some stats can penalize a QB of a team with a good run game. But look at their nearly identical completion percentage, yard per attempt, and QB rating (plus the same # of intereceptions.)