You can't view epub books in Kindle app but can in iBooks, Stanza, and BlueFire readers. I am sure there are other readers available too. I think that "non-Amazon" books cannot be placed in Kindle reading app by Amazon's design. But I am not a app designer so may be talking "out my butt", LOL
Can't you uncheck ibooks app in itunes and remove it from your ipad when you sync?
Actually I think you can directly transfer e-books from Calibre to you device without going through iTunes, but maybe not. It's been a while since I transferred books through iTunes.
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