I not only do that, but the Catholic Church does, too.
To clarify: war against the Japanese aggressors was certainly a just war. There's no question in my mind, and I've never heard different from any moral teacher of any sort.
A war may be just in its inception (jus ad bellum) --- which was not only justified, but I'd say obligatory --- against the Imperal Japanese military --- but it must also be just in the way it is carried out.
In other words, the fact that a war was morally right to engage in, does not mean that everything done in the war has a blanket justification. Upright warfare on the part of the individual soldier and the military command, (jus in bello), is also a moral requirement.
This is very clear to most U.S. soldiers, since it is spelled out in the UCMJ: you don't do rape and pillage, you don't zero in on non-military targets (as the jihadis typically do) and you don't massacre civilians.
If you do such things, they are war crimes, even in the midst of an otherwise just war.
This is not a pacifist argument. I am not a pacifist and I do not defend pacifism.
I am also NOT saying that no collateral loss of life can be justified. It can be.
In a war like WWII, a whole lot of collateral deaths could be justified, because a lot of the Japanese war industries and military assets were located very close to, or in the midst of, residential districts where you had thousands of people living in highly flammable wooden houses, and any time you went for a miliary target with incendiaries, you could foresee setting large swaths of the city on fire.
I know that; it's collateral civlian deaths; and (within limits) it can be justified.
What I'm arguing is that if you're targeting a city as such -- as the Council said, if the act of war is "directed to the indiscriminate destruction of whole cities or vast areas with their inhabitants" --- that's not collateral damage, it's intentional destruction of noncombatants. And as such it is not a justifiable act.
The intentional choice of indiscriminate slaughter as a means to an end is, in the words of the Council, "a crime against God and man, which merits firm and unequivocal condemnation."
When has so pure an example ever happened?