Well, since Roguekiller is meant to resolve malware infections and is run only once, and can used to kill avast services, it would make sense to protect avast from being disabled via avast self-defense module. Roguekiller is not run at every system startup.
Avast self-defense is meant to protect avast from outside attacks.
If you don't want avast self-defense to be running when you run Roguekiller just disable it temporarily for the duration of your Roguekiller malware cleansing session.