Hm, I've heard of river rocks exploding in a campfire when the water in the cracks flashes into steam. If the fire is very hot, and the pressure builds up faster than it can escape, kaboom. I have a hard time thinking that a rock could heat up that fast in a pot of boiling water--the gradual heating would tend to give the pressure ample chance to escape. Not saying it couldn't happen, but it seems extremely unlikely.
However, I usually don't boil rocks or wood because most of my pieces are too big, and Mrs. Badger really hates it when I use her pans for that kind of stuff. I give them a good scrub with a wire brush and set them out on the south side of my house for a few days. The Wyoming sun takes care of the rest.
This is one music teacher's opinion. I am not a physicist, nor a hydrologist, nor do I play one on television. Ask your doctor if boiling rocks is right for you.