I've had the same thoughts when adding a small rock to fill in space in my display, I don;t think dipping the rock will kill off the bacteria that makes the rock "live" but most live rock is porous, so when dipping the rock in a product like ReVive/CoralRx the rock will soak in the dipping solution. If you want to dip the rock, I would suggest that you soak the rock afterward in a separate container, at least that way it dilute most of the solution, hopefully not contaminating your display.
I know that I have dipped frags that were on live rock plugs with Bayer and didn't rinse the frag enough, about an hour later I had a ton of dead bristle worms and amphipods floating around...a mistake I don't plan on making again...