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.
2) Cockpit doors need to be beefed up and maybe should have two doors like an airlock.
Certainly in future aircraft designs this should be done - but I heard interviews with people who said the cockpit currently depends on the cabin air supply. You certainly couldn't put an airtight airlock in. But the door can certainly be beefed up quite a bit. The current designs, you wouldn't even have to give them more than an anemic kick - and I've been on flights where there's not even a door, just a curtain.
3) If terrorists start killing passengers in an attempt to lure out the pilots,
Assuming this is in fact what happened, I don't think the "luring" tactic will ever work again, even without specific guidelines to that effect.
5) There was a discussion about the destuctive potential of firing a gun on board a plane at high altitude.
On the other hand, what's more destructive, a dead terrorist and a puncture and decompression, or a flying bomb? Even wthout special ammunition, I'd think the risk could be worth it . Non-puncturing ammo would of course still be a good idea.