Creating an OS X-style "alias" is not enough. I haven't tried the following solution (and I won't do it myself as my HDD is big enough, sorry), but the correct way to do this kind of jobs on OS X is to create a "symlink", or "symbolic link", which is a UNIX-style alias (read more about it on Wikipedia if you'd like to). To put it short, you type/paste the following commands into Terminal.app, one at a time (you will be making changes to your system files and you will be prompted for your admin password, which is pretty dangerous if you don't understand the mechanisms—remember to quit iBooks.app first, make backups, and be prepared for any damages):
sudo mv "~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks" "/Volumes/EXTERNAL DRIVE/PATH TO IBOOKS FOLDER";
sudo ln -s "/Volumes/EXTERNAL DRIVE/PATH TO IBOOKS" "~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks";
You should change "EXTERNAL DRIVE" to the name of your drive, and replace "PATH TO IBOOKS" with the path you want to store iBooks documents on your external drive. For instance, replacing "PATH TO IBOOKS" with "iBooks" simply creates a directory named "iBooks" under the root directory of your external drive with the iBooks data. Note that after doing this you won't be able to properly use iBooks without connecting the external drive.
This might or might not work, but I hope this helps.
(If this doesn't work, recover to the original state by quitting iBooks.app first, and type/paste the following into Terminal (you might again be prompted for your admin password):
sudo rm -rf "~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks";
sudo mv "/Volumes/EXTERNAL DRIVE/PATH TO IBOOKS FOLDER" "~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks";
This will most likely recover your original working state of iBooks.)
