Violence for self-defense isn't pacifism though. Pacifism is not "only use violence when it is justified".
That you recognize that violence can be justified (for instance, in self-defense) means that you're not a pacifist. That is okay, most people are not.
The author asserts that violence used to prevent additional violence is illogical. You and I both recognize that as false, as both you and I recognize the value that violence can have when it is used for self-defense.
But back to the main point, there is a world of difference between "self-defense" and "violence used to prevent additional violence". Self-defense is immediate: someone is punching you, so you punch back. The other thing... it doesn't have to be. In my mind, self-defense is justified. But self-defense is defined as "have no other reasonable option", and thus is fairly narrow. If you can negotiate, if you can protect your interests by deterring the enemy, if you can eliminate the enemy without violence, by say sanctions, etc. then you have options and it's not self-defense. Also, self-defense is not the condition where violence is the best option. It's only self-defense when violence is the only option.
Perhaps violence is justified when it's not self-defense, but I don't think you can call any first-strike "self-defense" in order to gain the high moral ground.
Their use of violence against the hijackers was not pacifist, and because they were not pacifists many lives, arguably countless lives, were spared.