Apple could kill this behavior with one change: allowing users to revert to an older version of the app at any time. By this, I mean nondestructively, if possible, and without having to provide your own old IPA.
I'd agree, but it's never going to happen, for a few reasons:
1. Apple doesn't want to discourage ads. They want devs to put in more ads -- with iAd, of course. I'm honestly amazed they haven't made a bigger push for iAd than they have, but I think it's fair to say they're not going to do anything to actively discourage it.
2. The other problem is that app updates are rarely done only to put in ads. They're usually packaged with bug fixes, security updates, compatibility fixes for iOS updates, etc. So you're essentially asking Apple to freeze the apps at earlier, buggier, and in some cases even less secure versions. Neither Apple nor the app devs are going to be ok with that scenario. Hell, as a user, I'm really not ok with that scenario -- I can't get updates to an app that i purchased anymore if I don't want ads? That sucks.
So yeah, not going to happen. The best way to keep it under control, honestly, is for the users to complain when it happens, enough for it to have a potential impact on the bottom line of the app developer.