How to delete iBooks.app
close iTunes

via terminal.app

sudo killall bookstoreagent
sudo tar -czf /Applications/iBooks.tar.gz /Applications/iBooks.app
sudo rm -fr /Applications/iBooks.app


keeps you a working backup, just in case you need it back:

cd /Applications
sudo tar -xzf /Applications/iBooks.tar.gz


there is no need to alter any other files, nor to play with LaunchAgents or Daemons. Once the App is gone, iTunes gains back the books functionality. I read some evil suggestions on the interwebs.