I'm glad it worked, for those of you who tried it.
Here's the step by step of exactly what I did.
1.) Stopped the bookstoreagent process.
2.) Moved its file to elsewhere (Documents) so it wouldn't start up again on reboot.
3.) Copied the new buried iBooks book storage folder to my Desktop
4.) Opened up iTunes, and added all those books back in from that Desktop copy of the directory
5.) In iTunes, used the Library Manager to copy all those books back into the iTunes directory for storage.
6.) Went back and deleted my Desktop copy of the iBooks storage, and iBooks for Mac, and the books in the new iBooks storage folder.
7.) Crossed my fingers.
8.) Opened up iTunes, saw all my stuff there, synced to my iPad, and was, yea, verily happified.
It worked for me, anyway. You would certainly have to close iTunes and restart it after stopping the bookstoreagent process for Books to return, but you'll also have to add books into iTunes for the Books tab to reappear. Just use File: Add to Library for that. After the tab is back, you can just drag and drop files onto it to add books.
I did have one weird thing happen. A pdf showed up in Music! Strange. But nothing awful happened.
I figure if someday iBooks is all fixed up and works well, they'll have a download of it available, and I'll reinstall it at that point. But I was miffed that there was no warning that the inadequate iBooks would take over all book management from iTunes if you simply opened it. Not cool at all. Irritating, in fact.
Anyway, I'm happy to have helped figure something out that's been helpful to others. Happy weekend!