And I'm not defending Apple, here. I don't like where they're headed. But I find this whole 'the program was written in my brain' thing ridiculous.
This is the Apple App Store. All apps require Apple approval before they can be sold. They can reject apps on whatever criteria they like. They have also demonstrated this is not a theoretical concern, either, by rejecting things for all sort of reasons that can't be said to be "objective". Apple graciously gives developers some guidelines on how they may make their arbitrary decisions, but, well, while I concede I have not read the developer agreement it is only because I'm about 98% confident without looking that Apple never actually agrees to do anything w.r.t. releasing your app.
Ultimately, "we don't want our vision compromised" is a smokescreen. It is absolutely true that if this is what they wanted, they could accomplish it simply by holding all apps to the same standard regardless of implementation techniques. This is all about lockin.
Now, if an open platform mandated certain libraries, but allowed you to distribute arbitrary executables, the UX argument would at least hold water, as lacking the strong enforcement mechanism of having absolute say over what you can run on your device means that falling back to the weaker enforcement mechanism of code would arguably mean something. (Something stupid, but something.) But Apple already has total control. Arguing about how their already-total control can only be augmented by this technical thingie over here is a smokeshow; taking control from "total" to "total" is a no-op, technically.
It's like saying "I need the original copy of that file." What, you want me to ship you the hard drive? All you really need are identical bits of information.
Oh, crap, I defragged my hard drive. Guess I don't have the "original copy" anymore after all.
Yes they can, they can reject any app they don't want and have rejected any app they don't want.
In fact, I think the whole damn thing would be better if there was just a standard disclaimer, "Yeah, we'll reject anything we don't like."