Yeah right. When the terrorists burst through the cockpit door and find totally unarmed pilots, the most important thing is they won't be distracted by trying to shoot the intruders. They'll continue to keep the plane at level flight right up to the time their throats are slit and terrorists reroute the jet toward the nearest prominent landmark.
Put a person in the cockpit whose ONE JOB is to keep the bad guys out. You neglected that little detail of my proposal.
BTW, this proposal involves the FBI training the pilots. Your assumption is that the idiots who can't hit the right house in a firefight will be able to teach the pilots to react from a position of tactical surprise and shoot the terrorists (and ONLY the terrorists) dead instantly while still flying the airplane...I must admit don't quite follow your logic.