This is particularly annoying for me since I keep my itunes media stored on my nas rather than duplicating everything on my different machines.
A little surgery on osx is in order, rip out itunes and install itunes 12.4.3 its available as a download rip out iBooks from OSX although to be fair its a reinstall of osx to put it back if you decide you want it.
With 12.4.3 your music artists will have a nice jpeg instead of a pink microphone and with the removal of ibooks your books will not be stored as folders under ibooks and remain where they are. Of course that means itunes will tell you you can't read epubs on your mac but you can drag a book to any suitable ereader app.
its a shame as a reader ibooks is pretty good on the mac but the option of storing all books on icloud or just 1 laptop is not acceptable. If you have another partition or drive or virtual machine you can always use that for ibooks and use your main os for management.
I use ibooks on the ipad drag and drop in itunes works. You can even use Airplay to display the ipad screen on the apple tv (i can read that from across the room). I don't expect Apple to allow us any way other than their way in the future but currently you can still rebel!