The more likely scenario given these days, is that the hijackers will take a hostage - cabin crew, or pax, and with weapon to the throat of the hostage, demand the cockpit door be opened. There might not be a direct physical threat to the flight crew. So the question is, do you assume that the hijacker is "2 sandwiches short of a picnic", and there may be some chance of retrieving the situation, or assume that he is of the same violent, fanatical type - such as the Sept 11th's WTC participants? It then would come to the decision "Would you consider losing the life of one (and maybe another), to save thousands? Or do you allow the hijacker access, on the offchance that NO-ONE will probably die?"
Whereas a plainclothed, armed, security agent seated in the aircraft won't have such a difficult decision - pop him off either way!