Hey I fixed mine! I was having that identical problem and deleting my iBooks database worked. Your books may appear in a different order but they'll all reappear.
I use Linux to delete my database; go into the iBooks folder and find and delete a file that starts with iBooks and ends with .sqlite. You may want to back it up first.
iBooks automatically regenerates the database if it gets corrupted so this is a pretty safe thing to do. Hope your performance went ok!
First, perform a Reset on the iPad (different from just restarting).
Hold down on both the Sleep and Home buttons at the same time for about 10-15 seconds until the Apple Logo appears. When you see the Apple logo on the black screen, let go of the buttons.
After the reset, go to "Settings" then "iBooks". Go to "online content" and turn it on. Try downloading from iBooks again.
Hope this answers your question!