It'll be interesting to see how the "duplicate functionality" rules of the App Store play out once Apple's ebook reader is available. They'll have to pry Eucalyptus from my cold, dead hands.
Nope, they'll just take it away, and there's nothing you can do. Enjoy the future.
iBooks is not part of the system software. There is no reason to believe that the duplicate functionality rule would apply, even it its most extreme interpretation.
Stanza is, several apps which have had the same thing happen to them are not however.