1) Pilots should have small arms in in the cockpit so that they could fight off anyone attempting to force their way in the cockpit.
That gives a would-be terrorist a known source of a gun aboard an aircraft. Training all commercial pilots in the use of firearms (practice, etc.) is almost a practical impossibility - for that matter, there are some people who you just would not want to hand a gun to, not necessarily because of being a security risk (hell, they're already in the cockpit, if they want to kill themselves they can already do it), but because they can't hit the broadside of a barn.
They addressed this in the interview too. The terrorist could take the guns from the pilots but then you have the situation of a terrorist without a gun trying to take a gun from an armed pilot. The odds are in the pilot's favor. The pistols would be locked in the cockpit so that when a member of the flight crew is strolling down the aisle, they can't be disarmed by a surprise attack.
Also, since most commercial pilots are former military, they should be trainable in small arms use. Furthermore, since the guns would be for the pilots' self-defence, good aim is not too crucial. They don't have to hit a terrorist at 50yds holding a stewardess as a body shield. They just have to stop a guy trying to breakdown a cockpit door at 2yds.