What I think a lot of people don't understand is Amazon's goal here is to push out the competition by selling ebooks at a loss. In many cases at a deep loss. This has been done many times before and has always ended bad for consumers. You know why? Because there will come a point in time when Amazon will have total control and will jack up prices and there is nothing you can do at that point... Now right or wrong, Apple forced Amazon to sell books at cost, yes you paid more, but it also allowed for more players in the market. There is a reason a lot of books are not ebooks, they don't want Amazon selling them for a loss.
You're right, it's much better to give Apple total control, because Apple doesn't have absurd markups on all of its products or anything like that.