Yeah, if you have to medicate the quarantine, you're medicating the Live rock. At this point, you might as well leave it. If you have no problems while the fish are in QT, great... just put the rock in your main tank with them. If you do, you might pull the rock it's self out, let it dry completely and then, after a week or two dry, put in your main tank. It'll reseed in there.
After this, though, leave the Live Rock out, or only put like one biggish peice that you can afford to loose. The fish might like something to hide around... though most folks around here I've read use large pipe fittings from home stores for that.