Suicidal folk are not generally the type to take violent action against other people. They will usually quietly, privately take their own life.
With another person on the flight deck, the latent suicide also knows that their actions are likely to be thwarted - either by the other pilot, or by the F/A opening the door to allow the other pilot back in, so there is not much point in the suicide even trying anything - they are unlikely to be successful.
The problem is that a suicidal person left alone in a locked secure flight deck could convince themselves that they are now 'alone' and that their actions will only affect themselves.
The solution is quite simple: Move the secure cockpit door rearwards so that the forward toilet cubicle becomes part of the cockpit. Then no pilot needs to leave the flight deck during flight, even for a comfort break. If passengers complain about there being no forward toilet or higher ticket prices, say sorry, but remind them it is for greater security. I don't remember them complaining when the locked cockpit doors were first fitted.
This will cost money, but until 9/11, most aircraft did not have secure locking cockpit doors, and as soon as the security flaw was recognised, action was taken. The threat of the latent suicide by a non terrorist was possibly unrecognised until this crash, but a solution exists and action can be taken again.