Stuart,

Here's what we do to get around the same problem.  Create a CLI filter rule similar to this:

Don't add disclaimer if it already exist and bypass adding for specific addresses:

no_duplicate_disclaimer: if sendergroup == "RELAYLIST" {

                             if NOT

(mail-from-dictionary-match("Dictionary-NoDisclaimer", 1)) {

                                 if NOT (only-body-contains("keyword", 1)) {

                                     add-footer("Disclaimer");

                                 }

                             }

                         }

The dictionary match contains a list of email addresses that we don't want the disclaimer added to.  These are text notifications sent to phones.

We have been using this since day 1 with our Ironport devices and have not had any problems with it.

Doug