Generally speaking, it's good policy to hang on to submissions for record-keeping, even if they're never used; that's the purpose of the Archive. As Editor, you can send a submission to the Archive, regardless of its status -- unassigned, somewhere in the queue, or even published. Go to the submission's Summary page and find the "Archive Submission" link.
Once it's in the archive, if you're sure you want to delete the submission, you can do so by clicking the "Archives" link, finding the submission, and clicking the "Delete" button. This will permanently destroy all records and copies of the article.
Open Journal Systems Team