To me -- and this is pure speculation -- this is Apple's equivalent of giving Amazon the finger. Amazon acquired Lexcycle back in 2009, and that this could be part of a series of moves by Apple to drive people toward the iPad and the upcoming iBooks software. I wouldn't be too surprised if Apple found a way to ban the wonderful Kindle app [iTunes link] from the App Store at some point in the future. Is Apple becoming the next Tammany Hall with Steve Jobs its "Boss" Tweed?
For now, to avoid losing USB sharing, remember not to do a bulk upgrade of your apps and avoid any future Stanza updates.