As ilyazhito says, yes the game clock is to stop, by rule, when a safety is scored.
However, conventional wisdom and practice for NCAA (and NFL) officials is to signal the clock to stop (S3), and then check with any other covering official(s) to ensure that they agree on the ruling, and to take that extra moment to process the action, and make certain of the ruling before actually giving the safety signal. Same with a touchback. Signal for the clock to stop, process the action, validate the ruling, and then give the touchback signal. On kickoffs, the deep officials (R, H, L in crews of 7 or 8, R and L in crews of 5) should take that time/opportunity to move into the field of play - more or less between the receivers and the onrushing kicking team players - to get the attention of the onrushing kicking team players, so they will stop their advance.
This is a very odd question, though. Where in the world is anybody getting the idea that the game clock would not stop on a safety? 3-3-2-c is very specific and clear.