I don't believe that it is possible to achieve this goal. The answer, if there is one, has to be in the licencing of the passengers in their fitness to travel. It is a concept that is as extreme as similar measures taken in wartime.
The aviation hardware specialists will be focusing on the aircraft's defenses, leaving the security to ‘other departments', what else can they do? Well, if I were to be asked about modifications to the flying hardware, I would concentrate on the acceptance of the people entering the door. Each and every one of them would have to be acceptable to the on-board system.
The concept of being pre-approved is easier said than done. If the airlines were to be burdened with the task, it would cost the industry more than it could afford, it has to be carried out and funded by governments internationally.
Still, ‘sleepers' or those converted to another faith, or perhaps people that have become angry to the point of illness, will be a risk. Perfect documentation, but their psyche changed in some way. Governments would have to be held accountable for the quality of the vetting.
Aircraft have a unique vulnerability, we can only protect them by precise vetting of every single person that enters them, services them, and delivers goods to the immediate area surrounding them. The cost to the industry will still be vast, but there is no doubt in my mind that this will happen, it's just a case of just what will it take to make it happen. I fear that it might be one or perhaps two more major uses of airliners as weapons before such a radical system is resorted to.
What I'm saying will be unacceptable to almost all the people that have a vested interest in the industry, but we all know that there is no totally foolproof way that we can stop the destruction of an aircraft, when the people doing it are fanatics.