Well, that's sort of what I'm driving at. Apple clearly has an agenda with this clause and its not 100% clear to the developer community what that agenda is. Do they mean things like PhoneGap are dead, or simply things that provide an alternative API (e.g. running apps via the Adobe Air runtimes). How about cross compilers? Does Apple really give a damn if you write something in Scheme and then have it transcoded into Obj-C? I highly doubt.
My point is that their agenda, while useful to know, mean nothing in the long run, because as long as that clause is active, Apple has the ability to enforce it capriciously.
Whether or not they "mean" things like PhoneGap are dead, etc., is irrelevant. The ability to kill any app because of its original source language is the important thing.
You do realize that "ability" was already there? They've always had full control of what they allow in the store, so this latest change is only significant in intent, not ability.