Hmm a simple workable solution atm would be to tune the save to disk functionality to be able to perform the same metadata magic that the direct import to iTunes used to. I have tried all sorts of exports and cannot get metadata to stick and update in the export files when dumped into iTunes. Now either iTunes is either remembering the first import and then overwriting all future imports of the same book (after deletion in iTunes) or the metadata isn't updating properly on export.
I've set the appropriate preferences to update metadata, I've also tried converting from epub to epub and also tried the modify epub plugging.
But exporting to a folder and dragging to iTunes would be relatively painless. Obviously non-ibooks readers are also an option but you lose the push updates to your multiple devices and page syncing.