I don't know how long they'd have to sit to kill everything, but I don't imagine things that are designed for saltwater would survive a day in pure vinegar? Yes, you should probably rinse them before readding them
Putting them in the oven is the same risk as boiling them. Trapped water and air inside the rock expands rapidly or converts to steam and causes the rock to literally explode. You might do it and get lucky, but I wouldn't. Do a google for boiling rocks, see how many 'omg it exploded and I just got out of the hospital' type threads you find.
Edit: as far as just killing things, someone said put them in the sun for a day or two. I vote that. Turn them throughout the day(s) to make sure they dry all the way through.