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I agree, I don't think there's currently a way to put ePubs into iBooks without using iTunes.
However, I have converted a number of books into ePub using Calibre and they all work fine in iBooks. So if this is how you created your files, I don't think you'll have any problem.
From what I understand, there are a few ePub standard elements that iBooks does not currently support -- the most notable are alternate font faces, and embedded fonts.
However, if your books don't require these features, then your books will probably work just fine. I don't think that Calibre can create books with those features anyway -- can it?
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