Is there a way to permanently remove the iBooks app from a device?
Unfortunately Apple does not allow you to remove the app completely, however if you go inside the app and delete all the books and PDF's the app should be less than 5mb.

(Which even on a 16gb phone is negligible)

To delete all books/PDFs:


Open iBooks
Make sure all books is selected in the top dropdown menu.
Click Select and select all books
Then delete


Then go to Settings -> General -> Storage and iCloud Usage -> Storage: Manage storage -> Find iBooks and it should be &lt;5mb

If you would like to hide the app completely iOS 9.3 has a new glitch that allows you to do this, video for that is HERE.