Exploding rocks is a very rare, but possible occurrence. One way to prevent this is to put the rock in the water before it gets hot and then after its boiled let it cool down naturally. I would use a lid just in case, but its not normally an issue.
If you were realy worried about it, you could try soaking it in a bleach solution for a couple days and then soak the rock in am overdosed dechlorinator solution for a day to get all of the bleach out of the rock.
Other people just use hot water and a good scrubbing.