Not used this myself, but reading the instructions in the config_extended file, if you set the blacklist_gracetime to 1, this will probably stop an unsubscribe message being sent.
# when a user unsubscribes they are sent one final email informing them of
# their unsubscription. In order for that email to actually go out, a gracetime
# needs to be set otherwise it will never go out. The default of 5 minutes should
# be fine, but you can increase it if you experience problems
$blacklist_gracetime = 5;
Using this method should avoid hav ing to make changes to the core code on later updates I would think.