That's not a good comparison. An iOS device is not like a book shop. The iBooks application is. Nobody's asking that you can buy Kindle books in iBooks, but you can't even buy Kindle books in the Kindle app because Apple would demand 30% of the book. If you open the Kindle app on Windows you can buy books in there and Microsoft doesn't take a cut of the sale. People would lose their mind over this. Why is Apple different?
But, at the very least, Amazon doesn’t prevent you from reading ebooks from outside their store on a kindle. They just don’t favilate their discovery. (Unless things changed since I last owned a kindle which was quite a while ago)