Clean the rock with soap and water, rinse, then place it in a container containing a 10% bleach solution for 30 minutes. Then rinse the rock well, and place it in a container containing pure water and let it soak for a couple hours. If the rock still smells like bleach, keep rinsing.
You can replace bleach above with a 10% ammonia solution for a slightly more effective cleaning process (kills coccidia), though you may spend more time rinsing.
If you want to use something a bit safer, and one that doesn't require rigorous rinsing, use a white vinegar/hydrogen peroxide solution to disinfect the rock (after cleaning with soap and water). Keep both liquids in two separate spray bottles, and then spray them both on the rocks surface in equal amounts. Let stand for 2-5 minutes, then your done. A quick rinse is all you need, as there are no fumes or caustic left overs. This combo is just as effective as bleach, if not more so, in a fraction of the time. You can use it to clean vegis too. Remember, keep the vinegar and the hydrogen peroxide in two separate sprayers, and only combine them on the surface you plan to disinfect. Premixing them before hand is no good.
Additionally there is a chemical known as chlorhexidine gluconate that is commonly used as a veterinary wound wash and disinfectant. Extremely safe, no fumes or caustic liquids, and doesn't need to be rinsed at proper dilution levels. Lastly there is a home brewing product called Starsan that is very effective, and doesn't require much rinsing. Very similar to the vinegar/peroxide combo above in that they use mild acids to kill pathogens very quickly.