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Sigil isn't a command line application, landed. It's an EPUB editor with a "proper" GUI. Not sure why you thought it was command line only, if you tried it? FlightCrew is an EPUB checker/validator which integrates with Sigil (since it was written by the same guy), and can be invoked from within Sigil when you have an EPUB open in Sigil, as far as I know.
The problem with getting an EPUB through Lulu and into Apple's iBookstore is that Apple have some (undocumented!) requirements that go beyond the EPUB specification. Such as no spaces in the filenames of the files inside the EPUB.
BTW, one reason for having a .epub file extension is that it makes it possible for an operating system to associate EPUB files with an EPUB reader, rather than a ZIP file manager. If the .zip extension was retained, there'd be no way of telling the difference between an EPUB file that conforms to the EPUB standards, and a straightforward ZIP file, which could contain anything.
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