Which messages are you referring to? If the are from using the Growl action, then you can just delete that action. Otherwise, the messages are split up into categories like file event and errors. You can't really disable them on a rule-by-rule basis but on a category basis.
The only way to do what you want is to have Growl not deliver any file event messages (if those are the ones you are talking about) and then on every rule you want to have Growl messages for, use the Growl action to send a custom one.