I believe you can simultaneously sell an e-book in the iBookstore and sell a non-Apple created e-book with the exact same content somewhere else. For example, a word document turned into an e-book on Amazon. Just don't try and sell your Apple created e-book on Amazon, that's all.
I can also speak fairly highly of the leanpub team's process. My wife and I are finding it less than perfect for our needs in producing a fiction book with both ebook and print-ready book needs, but appreciate the directness and promptness with which both Scott & Peter have been responding to us when we are raising issues with what we're seeing.
Better yet, their conversion is free with no commitment to sell your book on leanpub required. I'd happily pay for what they're providing for free because it's so damned easy.
In fact, you can even sell an iBook—just like the ones iBooks Author makes—as long as iBooks Author isn't the program you used to make it. The iBooks Author software will inevitably spawn FOSS clones, and other tools that already exist (a likely candidate is Adobe InDesign) will allow export to the same iBook format in new versions, without the same EULA qualification. You might even just author an iBook "by hand," just the way you're currently able to author eBooks—writing HTML and CSS yourself, and zipping the results. You'll be able to have your cake and eat it too, just so long as you avoid Apple's particular cake mix.