Reality is, in the Movie industry, Theaters' success is dictated by the studios because you can't find another Transformers to play in your theater for a cheaper price unless China starts replicating movies too. In the app world, you can go develop for other platforms. That means developers will probably have to raise prices for in-app purchases, to offset the percentage Apple's eating, or just flat out abandon the platform.
Whether apps will leave iOS or not is a reflection of how much the app makers need iOS and how much market power Apple has with app makers. If Apple sets the terms too favorably for itself, app makers will not make a profit, go to other platforms, and hurt Apple in the process. If app makers develop for various platforms but determine they can't make money on iOS, they will abandon the platform.
My point was simply that markets are good at finding equilibrium and that forcing Kindle to drop the link is a good outcome. With the link, Apple is subsidizing Amazon by giving it a free platform, free publicity, and a path free sales that compete with Apple's own product on its own platform; without the link, Amazon is still getting the free platform and publicity, and you can still buy and sync content through Amazon's web site.
I generally agree with Apple's reasoning about the links and in-app content: If your app is a value-added feature to another service -- Hulu, Netflix, the New York Times, whatever -- you don't depend on, i.e., need, the link in your app or in-app purchases. If you do depend on a link or in-app purchases to cash flow your business, you should compensate the platform that delivers those sales.
Can you imagine Angry Birds deciding to stop selling games through iOS and expecting Apple to allow users to unlock its games with codes that you buy from Angry Birds' web site? If you were Apple, would you consider that a fair outcome?