If you were correct there would be no need for this FAA special directive
220mph - the Special Condition is issued as a pre-requisite to certifying a new system (generally Special Conditions are issued when the FAA believes that the existing FARs are not adequate for certification of new or novel technologies - the 787 had a boatload). The 777 system that the FAA issued SC against is still in development and won't enter service for some time.
The current 777 does not yet have an "Onboard Network System" (ONS), and the flight deck avionics are not linked to the passenger accessible systems in any way. There is simply no way for someone sitting in the back to access the flight deck avionics - there is no link they could use.
There is a terminal for doing s/w updates - but it's in the flight deck. If a hacker has made it onto the flight deck, I think there would be easier ways to take over the aircraft than to download something into the avionics.