The 2 crew rule on the flight deck will only double(at least) the chances having the bad guy behind the locked door. He/She will have a plan to overcome the other one easily.
I don't agree with that view at all as the FAA has already had the second non pilot person in the cockpit during loo breaks etc rule for several years and there have been no suicides by flight deck persons incidents at all in that time.
Generally someone who acted in the way this co-pilot did acts that way because of the feeling of unlimited megalomaniacal type power that being in sole charge of a vital life preserving system of this kind overwhelms them with because it is a way to compensate for the frequent feelings of inadequacy, self loathing and/or lack of control over their own life that they often secretly hold. The various psychopathic hospital nurses and also Dr Harold Shipman all had very similar psychological motivations. So generally those who have taken this kind of action seem to be largely motivated by the very fact that they can do it in secret without being subject to the criticism of and comeback on their actions that they face in their day to day life.
However as the vast majority of pilots are still male and the substantial majority of flight attendants are still female and relatively slightly built the chances of them overcoming the remaining pilot on the flight deck seem to be relatively low. Also the ground security checks that crew are now subject to mean that in general they couldn't usually get a knife or blade or gun on board to allow them to overcome the pilot/co-pilot left without a major struggle, the outcome of which would be highly uncertain. Of course there does still seem a small risk that members of a terrorist cell might take employment with a small airline as both say a pilot or co-pilot and/or co-pilot and flight attendant and then wait until the day to arrive when they were both serving on the same flight.
However the one additional feature that could be added to all passenger aircraft and that would probably have avoid both this crash and the Helios crash is providing a means in the main passenger cabin for flight crew to always be able to contact either ATC or their control bases and for either ATC centres or an airline's main control base to be able remotely send a signal that would immediately release the cockpit door. On the other hand as soon as potential suicide terrorists know that these protections are in place they will undoubtedly tend to try to instead crash the aircraft and kill everyone on board by putting it it in to an immediate and irreversible stall (in the manner of Silkair Flight 185).
So the big question is really how many years will it be before we have aircraft where an auto pilot flight path cannot be set that will fly the aircraft directly in to terrain (surely can't be difficult with global GPS now available everywhere) and how long it will be before the flight crew cannot make any control surface inputs that the auto-pilot and flight management systems know will stall or crash the aircraft. And if we do reach that stage then there are still going to be aircraft that crash due to faulty software design or faulty vital components in safely controlling the aircraft (eg altimeter, Pito tubes or even an uncontained engine failure damaging vital flight control surfaces) that might have been able to be avoided had we still had two pilots on board with the ability to access full manual control of the flight (the Lockheed TriStar crash at Sioux City for instance immediately comes to mind as a case where with full automation the flight would almost certainly not even have got anywhere near the ground).
So in short there is no perfect solution that a determined terrorist may not get around (including hacking in to any automated remote control systems with malicious and malevolent intent for aircraft with systems designed to land the aircraft remotely in the event of dual pilot disablement) but one suspects that ensuring crew in the cabin can always contact ATC and/or the airline's main ground base at all times and providing the ability to send a cockpit door release signal remotely (from the ground) would both be useful initial steps in the right direction.