Glad that you pointed out the original meaning of the proverb. If they took the metaphor seriously, they would do everything they could to root out and throw away those bad apples, rather than saying a few bad apples are not a problem. The whole point of the original proverb was that even one bad apple IS a serious problem. Sometimes the best way to refute an argument by analogy is to work out all of its implications, as you have done here so artfully.