Indeed the pilot is worse off if he is disarmed. The terrorist is now armed. He does not need his own gun. If the pilot was not armed in the first place the terrorist would need to take his own weapon on board.
Therefore the carrying of a gun by the pilot is a double disadvantage - unless you can be certain that he will be able to use it affectively himself without the terrorist getting hold of it. I, and most others, are not convinced that the pilot could do so and it is clear from the arguments put forward on this chat site that the majority have thought the problem through.
I recently had the pleasure of going through Orlando Airport as a passenger. The security was chaotic. It was noticeable that the US emphasis on peoples 'rights' meant that certain groups of people had a more easy route through security than others. A terrorist can easily exploit this. I, being British, did what I was supposed to do, and suffered accordingly. If I had played the system I could have gone through quicker and more easily.