Another reason to think that maybe Google withdrew Apple's license rather than Apple dropping the app:
The death of the native app means that Google, and not Apple, will now control YouTube on iOS devices. By doing so, Google will now be able to implement their “TrueView” ads on all devices, and not just those running Android.
When Google releases their own YouTube app for iOS, it will include these premium “instream” ad units that they have used via their YouTube website since 2010. These ads are placed inside of videos and are only played when consumers click on them. As such, they are much more profitable to Google than more traditional mobile ads.
As of now, Google hasn’t been allowed to implement these ads on iOS devices, because Apple, through the native YouTube app, doesn’t allow them. However, once iOS 6 debuts next month, it will be a new game.