The issue to me isn't whether the clock should have been reset or not, the issue to me is whether or not the clock should have ever been started. Here's the rules on injury timeouts in the final 90 seconds:
"f. 1. If the player injury is the only reason for stopping the clock (other than his or a teammate’s helmet coming off, Rule 3-3-9) with less than one minute in the half, the opponent has the option of a 10-second runoff.
2. The play clock will be set at 40 seconds for an injury to a player of the defensive team and at 25 seconds for an injury to a player of the offensive team (Rule 3-2-4-c-4).
3. If there is a 10-second runoff the game clock will start on the referee’s signal. If there is no 10-second runoff the game clock will start on the snap.
4. The 10-second runoff may be avoided by a charged team timeout if available.
5.There is no option of a 10-second runoff if there are injuries to opposing players. (A.R. 3-3-5-VIII and IX)"
I added the bold section, but that is a direct quote from the 2013 NCAA Football rule book. Michigan had an injured player in the final 90 seconds, so there was an injury timeout. Akron opted against the 10-second run-off, so the clock should have started on the snap rather than on the ready for play.