I never cull fry. I don't see any reason why something shouldn't live, just because it doesn't 'look right'. If they have a serious problem, usually they will die. If they seem in pain, sure, I'll euthanise them, but that's it. I've had Guppies live their life, happy as can be, with only one pectoral fin. It never bothered them.
If I ever did, I'd use clove oil.