When Preview doesn't allow you to save a file, nor 'Save as PDF' (nor open in Preview) from the print dialog, you can still use 'Mail Selected PDF Document' from the File menu.
Mail will then open a new message with the unprotected document as an attachment. The unprotected document is buried deep inside the private/var folder but can simply be opened in Preview by clicking on it in the mail message and then saved (unprotected) wherever you like.