Is Just War only ever a theory?

In her chapter "Where is Your O God?," Lepore elicits proof that the United Colonies declared "the said warr doth appeer to be both Just and Nessesarie" as well as other colonial voices as a means of justifying the increasing involvement of the other colonies to aid Massachusetts Bay in King Philip's War (107). Lepore explains that historically they would have derived their just war traditions from Grotius and his idea that war is not lawless. He grounds his idea in adherence to the principles of "the law of nature" (reason and logic) and "the law of nations" ("legal and moral principles") (108). Grotius also gave the principles of just cause (jus ad bello) and just conduct (just in bellum) as to the evaluation of war. 

I will not dive into the argument of whether or not the Native Americans were fighting a just war, because Lepore does not cite any major examples of their claim to a just war or their adherence to just war principles. However, I will argue that while the majority of the colonists considered themselves to be fighting a just war based on the laws of nature and nations, they were not based on their conduct (jus in bellum). Lepore cites examples of unfair trials of prisoners of war, imprisonment of innocent "praying Indians" on Deere Island, the captivity and torture of innocents including Philip's wife, and numerous captives (innocent or not) sold into slavery (141-151). The colonists however continue to adhere to belief in their justified cause. 

Lepore notes some scholars view that King Philip's War "was an archetype for all Indian wars to follow" (177). I would venture to say that it is an archetype for many or possibly all wars in the questionable adherence to just war principles although claiming justification. That being said, is just war only ever a theory? What factor does religious or "sacred" violence play in that possibility?

Lepore, J. 1998. The Name of War: King Philip’s War and the Origins of American Identity. New York: Vintage.