Apple is not blocking you from purchasing an ebook via Kindle's app. Amazon has chosen not to include this functionality in their app because they don't want to lose money on sales through their app.
Amazon is choosing to sell via iOS devices. They did fine before the iPhone was released, and I doubt having to forgo the sales via IAP is making a dent in their non-existent profits...
Here's a game. Go to Amazon, tell them you want to become one of their merchants. See how far they'll negotiate with you regarding their cut of your sales...
iOS is Apple's platform, just as much as Amazon is a platform for sales. Apple has just as much right to control it via rules and fees as Amazon does.
