iBooks 1.0.1
Apple has released an update for iBooks on OS X 10.9 Mavericks, with version 1.0.1 claiming the usual unspecified “bug fixes and improvements to performance and stability.” We did notice, however, that the update does not fix the category assignment bug we examined in “Managing an iBooks Metadata Mess” (6 November 2013). The update is available via Software Update. (Free, 14.7 MB)
I suspect that it also doesn't fix the #1 problem with iBooks, which I believe you've noted. That's the utterly silly idea that any ePub document opened must be added to iBooks library. I hated that with Adobe's Digital Editions. I hate it with iBooks.
This wouldn't be that hard to fix. If an ebook doesn't have DRM, the app should assume it shouldn't be added to the library. For those cases when it should, offer an "Add to library" option on the File menu.