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.
In the Hindu religion, one can[not] have freedom of speech. A Hindu must surrender his freedom of speech. He must act according to the Vedas. If the Vedas do not support the actions, instructions must be sought from the Smritis, and if the Smritis fail to provide any such instructions, he must follow in the footsteps of the great men. He is not supposed to reason. Hence, so long as you are in the Hindu religion, you cannot expect to have freedom of thought
The sacred texts of human history from all over the world, can never be perceived by the rational mind as texts of historical accuracy. They can only be a glaring representation of the traditions and ideals of the people. Now, it is up to the rational mind, to analyze those texts and thereafter consume the good elements from them, while discarding the rest.