IME I try to get rid of the critters, but leave the bacteria in tact. I do this by "cooking" the rock. I just feed the cooking tank pure ammonia to keep the bacteria alive, and any pest critters, they don't make it through.
The anaerobic bacteria in the rock is what converts nitrate to 02. If you do decide to bleach the rock, just plan to compensate for the nitrate removal another way.
JME
Curious, Brad, what pest did you end up with?