to answer your question about medications killing the bacteria in your rocks/filter - the answer is only if you use medications that kill gram negative bacteria. The nitrobacter and nitrosoma bacteria families are all gram negative, so broad spectrum anti-biotics that are lethal to both (like tetracycline) can shut down a bacterial filter. Erythromycin is only toxic to some gram negative bacteria and is specifically targeted to gram positive bacteria, so it can be dosed with a measured sense of security that it won't reset your bacterial filter to zero, though it might cause some instability.
I'm not aware of any common ich treatments that fry beds of nitrosoma and nitrobacter bacteria, though some of the more noxious ones might just kill everything except the fish. I don't think most copper treatments affect the bacteria bed either.
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