I think the larger "issue" is that the phrase colloquially means the exact opposite of the original observation, that a bad apple MEANS the bunch is spoiled. It's worse because this changing of the meaning is perpetuated by those same bad apples themselves.
"the proof is in the pudding" is a much more benign change. It's literally just a shortening, but no meaning is lost... if you want the proof, you'll find it in the pudding (implying you should try the pudding to verify your assumptions)
"Literally" is another word where the meaning changed from being the literal opposite of what it was "meant" to originally mean, not sure one is "worse" than the other. It's just change, which will continue to happen.
I would argue that the meaning has never changed. There is just an additional slang variation used by a subset of English speakers. Much like “wicked” was once slang for “good” and how Londers don’t literally ring people using the bones of dogs (“dog an bone” Cockney rhyming slang, in case the reference doesn’t translate).
"the proof is in the pudding" is a much more benign change. It's literally just a shortening, but no meaning is lost... if you want the proof, you'll find it in the pudding (implying you should try the pudding to verify your assumptions)