#1 is a bizarre argument. I can't weed my garden unless it is already free of weeds?
With 3.3.1 Apple is trying to control the overal UX. They can't reject bad music from the iTunes Store, but they can enforce basic encoding standards, so the music doesn't sound like crap for reasons other than the artistic content.
When they removed the "sexy" apps they were using a rule that could be made specific and enforced consistently. The picked adult content because of the peculiar standards that humans (and especially Americans) have when it comes to sex.
Or maybe it's really difficult to phrase a definition for "college humor".
Come to think of it, so does every headline I've ever seen about an app store rejection.
Clearly, though, the fact that the app store is already flooded with low-quality applications is indicative of the fact that Apple hasn't been doing that, which makes that justification seem totally bogus: if they really cared about low-quality applications, they could have done something about it long ago without restricting cross-compilation techniques. And if they wanted to put a stop to it now, they could still do it without restricting cross-compilation.
So to extend your analogy: if you want to weed the garden, then pull the weeds already. No need to have this strange level of indirection that will result in removing only a small number of the weeds while also eliminating plenty of flowers.