You can make a backup of your iPad, then sync it, and if this wipes out your data, restore the backup. But I'll admit it's a bit scary.
One thing that I forgot to mention: my suggestion works for books that were added to iTunes. You don't need to connect your iPad to try it, but of course you need to sync your iPad to update the titles on it after changing them in the iTunes library. I don't use the cloud sync option and I don't know how it works with books you add manually to the iTunes library.