Welcome to the Apple community.
The books are not actually in your iCloud storage, they are links to the books in the Store. What you are seeing is your purchase history and as such cannot be deleted.
You can however hide your purchases, which you can do from the QuickLinks > Purchased option from the main page in the iTunes Store on your computer.
Alternatively, create another category in iBooks and just put the books you want in there and ignore the purchased books category.