Just War theory is extremely fungible. Although you allegedly subscribe to Thomas Aquinas' machinations you then punt when the rubber hits the road ie "was Bush War 2003 just".
The killing of your fellow man (by the teachings of Jesus Christ) is an unambiguous wrong. Jesus did not speak to many topics in detail but the notion of Christ "endorsing" a war with mortal weapons is ridiculous.
By the description of Thomas Aquinas it's quite debateable whether the invasion of Afghanistan was "just". Why?
1) Bush did not exhaust ALL other options before launching his attack.
2) Arguably it was tacitly sanctioned by the UN . . . then again Bush doesn't consider them an "authority".
3) Arguably attacking Afghanistan did address an injury . . . with the notable exception that the "people" that truly wronged the US were all Al Qaeda NOT Afghanistan. Clearly, Bush made no such distinctions b/c they "intentionally" avoided going after Al Qaeda cells active in the Kurdish areas of Iraq.
4) There was little doubt that we would "win" so Bush easily clears ONE hurdle of the just war theory. Granted, it's quite obvious that Iraq is a whole different ballgame. Plus the very notion of winning a war on terror . . . by killing a bunch of people is suspect by definition.
5) Ultimate goal MUST be to re-establish peace . . . a peace "preferred" by ALL. Although suspect . . . I'm willing to give Bush that one when it comes to Afghanistan. Granted, it was quite a poo-hole before the war so arguably that was a low bar.
6) Violence MUST be proportional to the injury suffered. If you choose to measure the insult in lives then it's quite obvious that the Afghanistan War was clearly disproportionate. By definition, Iraq is off the chart.
7) Weapons must discriminate between combatants and non-combatants. The earliest iterations of Just War theory arose during periods where combat was quite personal. But no one can reasonably argue that technology has a bearing on what is morally correct. Dropping JDAMs in the city, cluster bombs, land mines, AC-130 raining fire from the sky, etc etc are by definition . . . immoral weapons of war.