You can permanently delete Kindle ebooks on Amazon's site. Hold in mind that if you do so you you will have to pay to download them again. Unlike Apple, Amazon will let you delete not only the book, but the fact that you own (and have the right to re-download) the book.
Books that show up in the Cloud section of your Kindle app are not on the iPad, and take up no space. So unless you have some other reason for deleting the book, don't.
To permanently remove a book from your Kindle library, go to Amazon.com, select your account, choose Manage Your Kindle, and sign in. The action button/menu to the right of the book includes a Delete from Library option.