Check out the draft Part 91 rules about firearms below. It would seem CASA is being taken out of the loop and you as pilot in command will just have to write yourself a note permitting yourself to bring your firearm into the aircraft.
Division 91.B.2 Firearms on aircraft
91.080 Bringing firearm into cabin of aircraft etc
(1) Subject to subregulation (2), a person commits an offence if:
(a) the person brings a firearm into the cabin of an aircraft; and
(b) before the firearm is brought into the cabin of the aircraft, the pilot in command of the aircraft has not consented, in writing, to the person bringing the firearm into the cabin of the aircraft.
Penalty: 25 penalty units.
(2) Subregulation (1) does not apply to a person who is authorised under another law of the Commonwealth to possess the firearm on the aircraft.
(3) Subject to subregulation (4), a person commits an offence if:
(a) the person possesses a loaded firearm in the cabin of an aircraft; and
(b) before the person possesses the loaded firearm in the cabin of the aircraft, the pilot in command of the aircraft has not consented, in writing, to the person possessing a loaded firearm in the cabin of the aircraft.
Penalty: 25 penalty units.