I've done it before without any issues. It completely wipes out everything on that rock and makes it nice and clean. I just give it a good rinse and set it out to dry for a few hours. You can always add baking soda to the water after its done bubbling to neutralize the acid if that makes you more comfortable with the idea.
It's my favorite way to clean rock. I was once given a couple hundred pounds of algae and pest infested rock because the guy just didn't want to deal with it anymore. I brought it all home, put it in a bin with water and acid. 20 minutes later they were spotless. I didn't even get a phosphate reading after the acid wash.
You can even do a couple washes if you'd like. It just eats away at the outer surface of the rock but it's very minor that you won't even notice. Just remember to add the acid to the water not the other way around. Do it outdoor and wear rubber gloves and respiratory protection if you can.
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