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.
Worse off? It depends on your definition of worse off! Since you will die a horrible death either way, which is worse? The end result is the same. The bad guy has achieved his goal of taking over the aircraft. With the firearm in the hands of the pilot, the terr. has less chance of doing so.