Killing a bunch of Jihadis may be morally justified, to save humanity from their wrath, but it won't terminate Jihad for long. Jihad or Holy war would keep festering one way or another, until religious fundamentalism is eradicated from the human society. Until the whole humanity learns to scrutinize its most revered scriptures with the sharp tool of reasoning, Jihad will keep on striking over the world. If one does not have the basic conscientious capacity to refute the primitive textual verses of the scriptures that demand one to kill or torture another being for holding a different belief system than one's own, then that entity is no being of the civilized human society, it is merely a pest from the stone-age. No Quran, no Bible, no Gita, no Cow, is greater than the human self. There shall be hope for harmony and peace in the world, only when fundamentalism is destroyed forever. Harmony is not a luxury, it is an existential necessity of the species. And to achieve it, if a hundred Bibles have to be sacrificed, then be it. But for no Bible, Quran or Gita, can harmony be compromised.

~ Abhijit Naskar

As to the 'Left' I'll say briefly why this was the finish for me. Here is American society, attacked under open skies in broad daylight by the most reactionary and vicious force in the contemporary world, a force which treats Afghans and Algerians and Egyptians far worse than it has yet been able to treat us. The vaunted CIA and FBI are asleep, at best. The working-class heroes move, without orders and at risk to their lives, to fill the moral and political vacuum. The moral idiots, meanwhile, like Falwell and Robertson and Rabbi Lapin, announce that this clerical aggression is a punishment for our secularism. And the governments of Pakistan and Saudi Arabia, hitherto considered allies on our 'national security' calculus, prove to be the most friendly to the Taliban and Al Qaeda.Here was a time for the Left to demand a top-to-bottom house-cleaning of the state and of our covert alliances, a full inquiry into the origins of the defeat, and a resolute declaration in favor of a fight to the end for secular and humanist values: a fight which would make friends of the democratic and secular forces in the Muslim world. And instead, the near-majority of 'Left' intellectuals started sounding like Falwell, and bleating that the main problem was Bush's legitimacy. So I don't even muster a hollow laugh when this pathetic faction says that I, and not they, are in bed with the forces of reaction.

~ Christopher Hitchens

Now how does all this relate to Islamic jihad? Islam sees violence as a means of propagating the Muslim faith. Islam divides the world into two camps: the dar al-Islam (House of Submission) and the dar al-harb (House of War). The former are those lands which have been brought into submission to Islam; the latter are those nations which have not yet been brought into submission. This is how Islam actually views the world!By contrast, the conquest of Canaan represented God’s just judgement upon those peoples. The purpose was not at all to get them to convert to Judaism! War was not being used as an instrument of propagating the Jewish faith. Moreover, the slaughter of the Canaanites represented an unusual historical circumstance, not a regular means of behavior.The problem with Islam, then, is not that it has got the wrong moral theory; it’s that it has got the wrong God. If the Muslim thinks that our moral duties are constituted by God’s commands, then I agree with him. But Muslims and Christians differ radically over God’s nature. Muslims believe that God loves only Muslims. Allah has no love for unbelievers and sinners. Therefore, they can be killed indiscriminately. Moreover, in Islam God’s omnipotence trumps everything, even His own nature. He is therefore utterly arbitrary in His dealing with mankind.

~ William Lane Craig