Yea thats sounds a little risky. When I put rocks in my tank I usually throw them on a baking sheet in the oven at 400 degrees for an hour or two. This seems more effective as the rocks reach a temp twice as high as boiling. Also this way you dont have to find a huge pot for doing multiple rocks...they just have to fit in the oven.
EDIT: This process will not remove contaminants. Will only help to sterilize