Apple's not demanding a piece of every book Amazon sells, the agreement is that if Amazon offers in-app purchases then it must charge the same price it does elsewhere. There are 2 reasons for this, but Apple's primary concern is that if Amazon charges $9.99 normally and then charges $15 in-app, then it's forcing out-of-app sales. So customers can still buy the books through the online option but if someone wants to buy in-app for convenience then they should not be forced to pay a higher price or go the other route. Amazon is simply not being penalized.
And it does seem a little inconsistent that you're being protective of Amazon's profit when it's the ultimate beneficiary of the practice (larger reader base = more sales; you and I and the rest of the world can continue buying books through Amazon directly).
I read the policy a bit differently...
If you have an app
And you sell content for said app outside of the app
Then you must also provide an in-app purchase mechanism
Content purchased via this in app mechanism must be at the same or lower price than the same content purchased through other channels.
So, If Amazon sells content for the Kindle App on their website (they do), then Apple is saying that they must enable in app purchases. Of those in-app purchases, Apple gets 30%.
Apple is not saying that we have to buy through In-App store, but that we must be offered the option and that the in-app price must not be higher. The idea is that the in-App purchase will be the easiest for App users to get to, and thus many sales will be channeled through Apple.
If Apple gets 30% of the gross sale and the Publisher gets 70%, nothing is left for Amazon. For them to make a profit, they have to raise the price. Because of Apple's lowest price policy, they would have to raise the price charged on the website as well. That's bad for consumers.
I'm not sure that in-app purchases are going to be all that convenient or compelling for Kindle Books anyway. I rather prefer to buy from Amazon.com then direct them to deliver to the device I select.