Baking it would be a bad idea, the water in the rock would expand and either split them, or cause them to explode. Boiling your rock would be better, but it stinks and it would be hard to find a suitable container to boil them, since metal can be bad.
There's also 'cooking' your rock, which involves putting them in a rubbermaid bin out of all light, with saltwater. After awhile everything on them should be dead.
Anyway, there's no quick solution. Boiling your rock will kill everything, and you'd have to do your cycle all over again. If I had extra money around and it were me, I'd be tempted to setup a whole new tank and system (a 'budget' minded one, of course), transfer whatever livestock you have, and break down the old system temporarily. Completely empty the old tank of substrate and rock, put them away for cooking or boiling, or whatever is you're going to do, and wash the tank and all of the equipment with water and vinegar.
Then nuke the site from orbit; it's the only way to be sure!