How do I permanently delete books from iCloud?

You can't permanently delete any items from your purchase history, all you can do is hide them so that they don't show in the Purchased links for redownloading : http://support.apple.com/kb/HT4919 - with apps and iOS 7, after hiding them on my computer's iTunes I've been having to then log out of my account on my devices and then log back for them to be hidden on that device.

If ibooks that are only in the cloud are showing on the bookshelf in the iBooks app then you can turn that off via Settings > iBooks > Show All Purchases 'off'

Apple needs to make it where books can be deleted.

You can try leaving feedback for Apple, but I doubt that it will happen : http://www.apple.com/feedback/

Doesn't this take up iCloud space? If it does take up valuable iCloud space, then we should be able to manage that space by deleting old or unwanted files/books.

None of your iTunes purchases take up any of your iCloud allowance (or extra iCloud storage that you've bought), they are in addition to it