Let's accept it: we may make things gradually better, but there is no silver bullet that would solve all these problems.
To prevent attackers from muting all but the required majority of crew members, sensors all over the plane must be able to record any emergency code words spoken in the event of an attack, which will enact certain security measures (depending on the code word could lock or unlock the possibility to enter the cockpit, notify air security etc). This system should of course not be able to be deactivated.
And if you really wanted to make things sure, you could install majority-authorization buttons on every seat setup to be pressed by a percentage of boarded people within a period of mere seconds, which would allow the people on the plane to make a decision. For an attacker it is not possible to make all those people press the button, since he would not know who is not complying.
Of course you can also have some remote mechanism of unlocking, although the security implications of remote authorization and transmission of commands would be complicated to get right and open too many attack vectors.
Any procedure that aircraft crew is supposed to handle also needs to be something that is trained, memorized, and practiced regularly. Certain simplicity is ideal.
Thus rendering the doors essentially useless, as hijackers threaten to kill passengers one-by-one until the crew (who will generally outnumber the 1-2 people in the cockpit) open the door.
For instance, to replicate someones fingerprints all you need is a high res photo of their hand from a distance.
Then the airline will move on in the arms race by responding with a fingerprint reader that wants to have a pulse in the finger, and then it doesn't work when the user is in distress and has an extremely high pulse. And then there is an accident and we the armchair security experts come up with more bright ideas.
Last time I had an airline meal, even in first class, the knife "blade" was hard rubber mounted on a blunt metal handle. It could barely cut the food cleanly, never mind someone's finger.