I would not worry ab out Apple and their subscription service. That affect only iDevices
eBooks you buy from Amazon are going to be available on your kindle and on your computer and Apple has no control over that. Besides, I read today that the DOJ is taking a look at this whole Apple ordeal. Nothing official but we will see how this goes. I personally thing that there are going to enough entities that will refuse to play by Apple's rules and Apple is going to have to retract their gouging techniques... or vendors will come up with creative ways to provide content on the iDevices by other methods. Maybe they will embrace the JailBreak community.
As for backing up your books, you will always have access to them from amazon but you also have the ability to download them into your computer at will