I can confirm that the problem is caused by the new SIP (System Integrity Protection) built into El Capitan. I had been told before that iBooks was not affected at this level, but it would appear that Apple changed their minds on that one.
So....
- quit iTunes
- kill the process com.apple.BKAgentService
- delete /System/Library/PrivateFrameworks/BookKit.framework/Versions/A/XPCServices/com. apple.BKAgentService.xpc
- use appzapper to remove iBooks
- delete ~/Library/Containers/com.apple.BKAgentService
- delete ~/Library/Containers/com.apple.iBooksX
- empty the trash
- restart iTunes
For me to action the instruction at stage 2., I had to disable SIP first.
Boot into Recovery Mode using CMD + R, then select Utilities from top menu
Select Terminal, and then type following and Enter
csrutil disable
Then Reboot system
Then go back and try Stage 2. (I'm sure you can probably do all this from within Terminal in the first place, but I'm not that knowledgeable)
Follow stages through until stage 7. I then rebooted again before trying Stage 8. just to be sure, and can report ALL IS BACK AND OK!!! 🙂
****By the way, I personally didn't find the listed item in stage 6. (maybe because I hadn't actually opened iBooks??)****
For my own system safety, I then chose to boot back into Recovery mode using CMD + R, back into Terminal and then typed csrutil enable, to enable SIP again to protect from the potential nasties.
Hope this helps anyone who has encountered problems since the recent El Capitan release.