The theory of just war is no longer a viable theory. Yesterday I attended a lecture by an important ethicist who spoke very dumbly about Just War theory and terrorism. The theory is mostly one thought about by Catholics following in the tradition of Augustine, and lately by fans of Michael Waltzer.
Unfortunately, the theory depends on a few things that can no longer be counted upon. Modern warfare in the middle east is not symmetric, in the sense that we know where the battlefields are, there is no clear distinction between soldier and civilian, a human shield is no longer your enemies civilians that you are using for protection, but your own. There are new presuppositions about what counts as an army, and a target. All of this goes in to the failure of just war theory.