How to move from iTunes book library to iBooks app
I finally managed it by re-creating my iTunes library as mentioned here: http://support.apple.com/kb/ht1451.

After moving the .itl file I also moved the Books folder under iTunes Music.

It takes quite some time to import, depending on the size of the library, and it will finally warn that some items could not be found - which is obvious after deleting Books.

After that the contents of iBooks appeared in the Books sync tab.

Edit: Unfortunately, all my apps for my i-devices were gone, too. I had to manually transmit them device by device via the menu item File&gt;Devices&gt;Transfer Purchases from (device name). This step is clearing all the apps that I haven't synched to any of the devices at this time, which might be good or bad. However, I can download them again if I'm in the need for that.