Use 'cl' to our heart's content. Try to minimize use of 'cl' at runtime, ultimately cut it out. "Stop using 'cl' right now, loading it is already breaking stuff!"
I think this is a political issue more than anything else... the GNU Emacs maintainers don't like cl to the extent that they create warnings for it; the XEmacs folks don't.
I'm not sure to what extent cl.el modifies emacs-lisp behaviour; in Common Lisp you would have to use a macro, or wrap the defun in an eval-when clause :-)