In order to delete a book from the Class Shelf that a student added, you need to delete all of the work associated with that book.
From your Dashboard, click the student who added the book. From the Text Table for that student, click the View link next to any quiz or journal activity listed to the left of that book:
On the next page, click the "remove" link to remove that quiz or journal activity. Do this with all the work listed on the text table for the book you want to be removed. Once there is no work for that book, it will no longer be listed on the Class Shelf.
Note: For Whooo's Reading School account, you will also need to delete any reading logged for that book. See Edit Logged Reading.