The current strategies for dealing with skyjack were formulated during the early 60s and seventies, where the skyjackers were either political refugees "Take me to Cuba!" or people willing to make a political statement by by diverting an aircraft to a remote field, then destroying it on the ground. Some were merely disturbed individuals looking for attention.
Under that paradigm the advice to "follow whatever directions the skyjacker gave", while attempting to alert the authorities on the ground made eminent sense. The skyjacker had the advantage of surprise, was mentally prepared for violence, usually armed and had access to hostages in the cabin, while the pilots were taken by surprise, strapped into seats with their backs to the skyjacker and hampered as they also had to ensure the safe flight of the aircraft. A physical response while airbourne would always have a very low likelyhood of success, while dealing with the situation on the ground, with ground assistance, maximised the chances for survival of all on board.
Under this new paradigm - suicide skyjackers using the aircraft as a 200 ton missile with inbuilt hostage protection while in flight, may require a re-think of the strategies in dealing with skyjack.
In the USA in the early 60s and 70s - before significant ground security checks at airports, pilots began to arm themselves as several pilots were killed at that time.