That bites, I would not even trust leaving it in the aquarium. I've see guys have to completely tare down everything because they thought treating it in the aquarium would do the trick and it came back even stronger. You can remove the rock and still have traces in your sand bed as well.

My thoughts, take all the rock out and bake it in the sun for a couple of days. Lots of folks have started giving their rock acid baths also. That way you know the rock is going in with nothing on it a live at all.