It would be easy to add a nice electric-right-paren function to clojure-mode that would be bound to ')'. It would always insert the right kind of a closing paren.
paredit-mode (http://www.emacswiki.org/emacs/ParEdit) already provides a lot of functions for manipulating s-expressions, including keeping track of your braces.
Actually, I'm wondering why that doesn't already exist there. (Just checked.)