There is a very easy solution for the NCAA to eliminate the potential use of defensive penalties to run out the clock on end of halves and end of game.
On any defensive penalty that occurs in the last 2 minutes of each half (after the new 2 monute "warning"), the offense should have the option of having the clock reset to the time on the clock at the beginning of the play. That handles any potential penalty to gain an unfair advantage and helps protect the integrity of the game. This should have been implemented already to avoid these types of potential situations. Very easy fix that could be implemented immediately.