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I think the real error is this:
IOError: [Errno 21] Is a directory: u'/Users/kimberlynorton/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks/Books/22651C84B5200231F2568B76D294EC4E.epub'
which means that iBooks has unzipped the epub into a folder whose name ends in ".epub". So you are asking calibre to try to load a folder and not a real zipped up epub file.
I have no idea why iBooks does that (giving a .epub extension to a folder).
Perhaps try dragging and dropping that folder onto an epub zip tool and try loading the result?
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