The error only appears when you try to open DRM protected books.
To get rid of it: Add http://repo.insanelyi.com repository in Cydia and search for iBooks Fix. Install it and all will be working again.
Update: If you used Greenpois0n to jailbreak, it's now been updated to fix the bug. All you do is run Greenpoison jailbreak again over the top of the old one. There's no need to restore.
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