You could also try deleting all books from the apply connecting it to your computer's iTunes - either change your sync options or use the Books tab under the 'on my device'' heading to select and remove them. If you haven't already got copies of all the books on your computer's iTunes then first do File > Devices > Transfer Purchases to copy them over (you might be able to redownload ibook purchases, but any item could be removed from the store at any time), and if using a Mac with Mavericks or Yosemite on it then do File > Move Books From iTunes in its iBooks app.
If the app then opens with no books in it then try syncing them back