The easy solution to all of this would be for all of the ebook sellers to add in app purchasing to their reader apps. They should add a 30% surcharge to all in app purchases but still sell their content for normal price elsewhere. This would allow them to conform to the Apple guidelines and still keep their customer base happy.
The Kindle app is in violation and will likely be changed. While I wish Amazon could get away with your surcharge idea, I'm betting Apple has already plugged that loophole.