I was also watching the game and was wondering what the ruling was. Here are the two possible rulings taken from the NCAA Rule Book:
Rule 6-2 (d) – Immediate Dead Ball, Runners Return
d. If a batter swings and misses a pitch and the backswing is so forceful
that it hits the catcher as the pitch is caught, or if the batter hits the ball
again, the pitch shall be called a strike, the ball is dead (no interference)
and no runner shall advance on the play;
(1) If the interference occurs in a situation where the batter normally
would become a runner because of a third strike not held by the
catcher, the ball shall be dead and the batter declared out. (No runner
shall advance on interference.)
(2) If the catcher has possession of the ball and is in the act of throwing
or preparing to throw and the batter interferes with the catcher, the
batter shall be declared out provided the throw does not retire the
runner. If the interference occurs after the third strike, the batter and
runner shall be called out and it will be ruled a double play.
Rule 7-11 (f) A batter is out when:
f. The batter intentionally or unintentionally interferes with the catcher’s
fielding or throwing by stepping out of the batter’s box or making any
other movement that hinders a defensive player’s action at home plate.
PENALTY for f. —The runner(s) return to the base occupied at the time of
interference;
I really don't want to criticise the umpire for it may be an approved interpretation; however, it seems like Rule 7-11 (f) is more applicable.