Here's my take on it. Apple's greed is amazing to behold.
It's not clear that it's about greed. Far more likely is that it's about control, control over the experience of their users. Apple has a direct motive to fully support the Kindle app on iOS, because the users of their devices want it there. iBooks just exists for users who can't be bothered to dive into the Kindle ecosystem. But also, Apple has a direct motive to prevent sketchy financial transactions from originating from within iOS apps. A couple of errant games that redirect users to a Russian mafia site to steal credit cards can very quickly remove any trust that people have in the App Store. Apple is mitigating this, at the very public cost to a handful of apps (Kindle, Google Books (or whatever), Netflix, etc.) But the bottom line is that in this capacity, Amazon, Google, and Netflix are all middlemen. Middlemen are going the way of the dodo in general, although today these three behemoths obviously provide a great deal of value to the end-user.
I don't use Kindle or Google Books or Netflix on my phone, so I'm not certain what the big deal is. If you have a Kindle account, is it really that hard to buy books at amazon.com rather than from within the Kindle app? Maybe it is, but the only effect this policy has had on me is to elevate the amount of trust I have with in-app purchases -- Only Apple will ever get the transaction details, and Apple has a pretty good track record with processing purchases.
I have a hard time finding fault with Apple's policy on this.