Arm the pilots? Of course! Most of those fine ladies and gentleman are former military. These people have gone through all kinds of training and background checks to get the job they have. I'd hope they take their job of getting us safely from point A to point B seriously, that should include dealing with potential hijackers in a lethal manner if needed.
The pilots and other crew (let's not forget there is more than pilot and first officer to make it fly) don't have to be armed with firearms. Stun guns, handcuffs, and pepper spray might be good ideas. (Maybe not the pepper spray, close quarters and all.) If they are armed with a firearm they should be loaded with ammunition that is unlikely to punch a hole through a bulkhead or damage vital equipment. (A round through a O2 tank might make for a very bad day.)
I've heard there have been some very successful tests with new ammunition that, while still very lethal, will fall to bits when it hits metal. I here the Air Marshals have been asking for this ammunition as they don't want to have to risk losing pressurization in the aircraft while subduing a bad guy.
With that in mind I'm not sure I want people to go onto planes armed. Just like going to a sporting event, a bar, or any other place where there is many people in a tight space and alcohol is available there is security checking for weapons. I don't want some yahoo to check if his "Glock 7" is on safe in the middle of the flight and accidentally putting a hole in the window.
I remember when going to a soccer game that the security was looking for glass containers, whole fruit (like apples and oranges), or other items that could be thrown onto the field. (Maybe that is why I couldn't bring my water bottle onto the plane, they were afraid I'd throw it at the attendant after blowing the whistle. :banghead
They were looking out for things that could injure others. A plane should not be any different.
Unlike other "gun free zones" in an airplane someone isn't going to suddenly appear with a shotgun while cruising at mach 0.8 over the north Atlantic. What they will have to deal with are people threatening others with improvised weapons or shear strength. Taking firearms from immediate use of the passengers should not be considered putting them at risk of another shooter.
I remember a friend of mine, older than myself, mentioning that he used to bring his rifle on board a plane while going on hunting trips. While I was amazed at first that he was allowed to do such a thing I realized what little risk it posed and now I don't see a problem with that. Treat the transport of a firearm in a plane like they do when traveling in a car, it must be unloaded and locked in a case, once on board it is to be placed in storage until you leave. That way the firearm is where you can keep track of it, since it is a valuable item much like a laptop, and you can then arm yourself as soon as you get off the plane.
While we can talk about this all we like I doubt the powers that be will all of the sudden think sanely about airline security.