Conjecture: End users can be confident everything that they purchase in an app is tied to their iTunes account. Purchasing an Amazon e-book using the Kindle app means the end user — who is not the most tech-savvy — needs to have an Amazon account and they need to be aware that anything purchased in the Kindle app (and only the Kindle app) doesn't get associated with their iTunes account, which is a different behavior than every other app on the App Store.

Of course, the 30% cut that Apple wanted to take most likely had something to do with it, but there is a good reason to forbid developers from implementing their own in-app purchases.