One part of this solution might be these Applescript that unpack and repack an unencumbered (no DRM) ePub file:
Unpack the .epub, edit the .xml and other text files contained therein and then re-pack the .epub file. So, what would have to be added to BBEdit in order to support the EPUB standard XHTML markup?
The Automator ePub workflow described
here works well but you'd occasionally want to be able to use the scheme described above to unpack the .epub and then edit with BBEdit.
Then, too, the Pages app from the iWork suite for MacOS X has just gained the ability to export EPUB files. Maybe that lessens the demand for BBEdit support?