Bitcoin apps are a challenge to this. Say if Amazon made a wallet app that happened to let you buy EBooks?
http://store.apple.com/us/product/H8332LL/B/square-credit-ca...
The difference between bit coin and the paypal app is that bit coin is cash. If I embed bit coin code in say, the Kindle App, I can make purchases that Apple wants a 30% cut of.
So no, it has nothing to do with iTunes, and nothing to do with Apple's 30% cut. It's just a completely made-up reason.
On the other hand, if you're selling physical products, you're not allowed to use Apple's IAP. I was actually surprised when I read this, but the review rules did state that last time I looked.
Using an app to manage a payment system that's external to Apple is quite legitimate. That's why the PayPal app exists. And I would wager that Bitcoin apps would fall under the same general category, of being things that happen outside of IAP, and therefore the reason they're getting pulled from the store has to do with something other than the IAP rules.
The iBeacon is a clear step in that direction and besides it's not like Apple is upfront about it's business, iBeacon was in Apple devices for two years before anybody found out about them for crying out loud. They know their endgame and are always working towards it.
That being said, they will loose this one