Do you have a copy of the old version somewhere ? If so then you could try deleting the current version from your computer's iTunes and adding the old one via File > Add To Library and see if it then appear in the Apps part of your library - you can then delete the version from your iPad and try syncing that one.
If you have a Time Machine backup, this is how I restored to iBooks 3.1.3:
In your Music folder, open the iTunes folder, then iTunes Music, and then open the Mobile Applications folder.
Enter Time Machine
Go back "in time" until you can locate the iBooks 3.1.3.ipa application file
Restore the file to your desktop
Delete iBooks from your device
Open iTunes, and delete ibooks 3.2
Add the iBooks 3.1.3 app from your desktop to the iTunes library (Add to Library in the Files tab)
Connect your device to your computer, access it through iTunes and, in the Apps tab, click the install button beside the iBooks app
Apply and sync
This worked flawlessly for me, averything was where it was supposed to be and I was back to the familiar iBooks I love...