How do I open an EPUB from an email in iBooks on my iPad?
In all cases I have tested, iOS recognizes epub files and will offer to send them directly to iBooks.

I have tested this from the email all, dropbox app as well as mobile safari.

Other apps like Evernote and AirSharing also are able to receive my epub files, so if you are not able to do this, perhaps it's an encoding issue or something about how the files are being attached to the emails and not necessarily a problem with iOS.