So the question of Apple being at fault for not having "clear, comprehensive guidelines" can't really be raised.( In this particular case.)
And so the headline is a bit sensational.
If what you're saying were true, Apple should have fairly quickly rejected it citing the grounds you state. Something else is going on.
And isn't it the case that there are already quite a few interpreted code exceptions already in place, e.g. Lua in games?
And with respect to the other thing, your bringing that up kinda proves what I said, doesn't it? :P