For those of you interested in the debate about a crew member in the Cockpit and if it would do any good, let us not the forget the lessons from Federal Express Flight 705
Federal Express Flight 705 - Wikipedia, the free encyclopedia
A Deadheading Crew Member boarded the aircraft with every intention of crashing it and even armed himself with handheld weapons but still failed to do so, in no small part due to him being outnumbered.
Keep this example in mind for those who think that having extra crew in the Flight Deck or even making sure there is CC in there to cover for a Flight Crew Member needing to use the facilities will serve no purpose.
With the remaining Pilot flying being in their Seat and the CC sitting in the Jumpseat I'd say it would be particularly difficult for the Pilot Flying to attempt to incapacitate the CC Member, it would be bloody obvious when the Pilot Flying tries to get up and do something as they should not be leaving the seat at all.
A CC Member might not be able to tell when you've done something wrong to intentially cause harm but they'll figure it out pretty quickly and at least it gives a far greater chance for the Pilot Not Flying to be able to regain access to the Cockpit and try to save them whilst the CC Member does their best to restrain the one causing the problem!!