You gloss over the point that this would have meant the hijackers would not have been armed with boxcutters but with their favorite firearms as well. At best this results in a bloody shootout.
Doesn't sound like such a plane would be hitting any buildings....
A bloody shootout would have been better than the destruction of the WTC and the deaths of thousands.
On 9-11, even the pilots were disarmed by government. Had that been different, your argument is demolished - no shootouts if the pilots have guns but the hijackers didn't.
Finally, after thousands of deaths, the government is backing off this particular prohibition - and thus tends to Libertarianism. This itself cuts against the premise of the article that Libertarianism necessarily fails and government alone can save us: government has thrown its hands into the air and is considering giving power of self-defense back to pilots.
In which case no plane crash into the towers. More than likely, it would never have been attempted.