How-to Fix Please restore with iTunes and reinstall iBooks
By 
There is a problem with the
configuration of your iPhone.
Please restore with iTunes
and reinstall iBooks.
Did you get this error when opening any iTunes store ebook using iBooks app?
If you have jailbroken device (iPhone, iPad, iPod) and getting this error when you are trying to open DRM protected books from iTunes store, you dont need to restore your iPhone with iTunes. It will remove your jailbreak, data, custom settings and any modifications.
According to Comex –creator of JailbreakMe, the app checks to see whether the device is jailbroken or not by trying to execute an improperly signed binary. If it works, the application knows that the device is jailbroken and the book will not opened.
Here is the complete comex’s tweet about iBooks app:
On Tuesday 15th February 2011, @comex said:
It seems that before opening a DRMed book, iBooks drops an improperly signed binary, tries to execute it, and if it works concludes that the device is jailbroken and refuses to open the book.
This is what the binary does:
int main() {
return 42;
}
How-to fix this iBooks issue without restoring with iTunes?
1. Add this repository on cydia: https://repo.insanelyi.com
2. Once done, search for iBooks Fix and install it to device.
3. Done.
The new greenpois0n update and sn0wbreeze already has fixed iBooks issue.
Cydia 
