I've had some success getting iBooks on iCloud to work on my iPad 3. I found that if I signed out of my usual iCloud account and into one with no books the iBooks app would not crash when it opened. As an experiment I loaded a couple of books to that iCloud account and they worked on the iPad just fine. When I signed the iPad out of that iCloud account and in to the new one, synched it as usual to iTunes, everything worked just as it should. To do what I did you need a mac with no e-books loaded in its iBooks application and a spare iCloud account.
1. Sign a mac without any books in iBooks into a fresh iCloud account
2. Select "use iBooks in iCloud" when prompted.
3. Sign the iPad into this fresh iCloud account, and select "use iBooks in iCloud" when prompted.
(Opening the iBooks app no longer crashed under this arrangement - adding a couple of e-books to the mac's iBooks got them successfully onto the iPad.)
4. Sign the Mac and the iPad out of the fresh iCloud account
5. Sign the iPad into the existing account with ebooks available.
(don't know if it's necessary, but I synched the iPad with iTunes at this point - iTunes copied books, though not PDFs, during the sync.)
6. Open up the iBooks app on the iPad - the entire library is present and functions as it should without crashes. New additions appear as books available in the cloud on the iPad.
Had this not worked, the next thing on my list of things to try was to wipe out my existing iBooks library and reconstructing it - adding a few back at a time.