Re; Yes, but...
We do know some real facts about the situation, and some of them are not what's represented in this story:
First, the policy is not to prevent booksellers like Amazon from selling e-books through their own channels. The policy states that "in-app" purchases must be done through the iTunes infrastructure. There are valid reasons for this, which I will mention below, but they are irrelevant: Amazon does not sell its books "in-app," they do it through their own site.
Second, the policy further states that if an application developer sells content through external channels, such content must also be available through the iTunes infrastructure as an "in-app" purchase. This does not limit choice, but expands it: Users must have the choice of purchasing through an external (and perhaps unknown) vendor, or purchasing the same through Apple (presumably trusted, if the user already has an iTunes account).
Whether Amazon will agree to this, is an valid question, but I can't see why they wouldn't. So far we know nothing regarding price restrictions, so it seems possible that Amazon can offer their direct sales at a lower price than the iTunes versions, and thus have an advantage. To presume that this is an anti-competitive stance rather than a user experience issue (more of this below) is premature and disingenuous.
To recapitulate, there are two separate policies here:
1. All "in-app" purchases must be done through Apple; purchases through other vendors can be done outside the app. Furthermore, All externally purchased content must be installed into the common file areas and not downloaded into the application package.
3. All externally purchased content must also be available as an "in-app" purchase through Apple.
Regarding the first two, there are some valid reasons why this policy is in place. The most important one is security: In-app purchases performed through external channels cannot be verified by the user to be performed through secured channels. Amazon knew this and did not argue the point, opting instead to have the Kindle re-direct the user to their own e-commerce site, so that the user can confirm that the transaction is done through a secure (HTTPS) transmission.
Then there's user experience issues: if an app downloads content within itself (by modifying it's package), the user will not be able to share the content between installations of the same application on different devices.