The first is to reconsider the distinction between "soldiers" and "civilians", and the "innocent" in a world of total war. Just war theory was created back when Augustine was trying to buck up the morale of Romans defending themselves against barbarians. The idea was that the Romans could justly engage in war to defend themselves, including killing barbarian invaders. But this justification didn't extend to non-combatants; say, the barbarian women and children. At that time, there was a pretty clear distinction between combatants and non-combatants. The guys with the swords were combatants, the women carrying children weren't. Moreover, the women carrying children were more a hindrance than a help to the invading barbarians. Armies back then lived off the land they invaded, and carrying along women and children only brought more mouths to feed. So the noncombatants back in those days added no combat value, and were truly innocent.
This state of affairs continued up until about the 18th century. Until then, the horizon of the average peasant was the end of his fields, and whether he would get a decent crop in that year. Wars between Kings didn't concern him overmuch, and he likely only learned the news of war only through an army (his King's or the enemy's) trampling through his fields. These wars were a matter of intermittent battles, between which things were pretty much indistinguishable from peace. The soldiers were armed with sword, pikes and arrows, none of which required a supply train or massive support from the home front. In a war like this, soldier and noncombatant have clear meanings.
Starting sometime in the 19th century - our Civil War is a good place - war began to change. It stopped being the occasional violent contest between armed minorities, and started becoming an enduring economic contest between nations. Soldiers were now armed with rifles and cannon that required extensive supply support in terms of ammunition and repair. A medieval army was good to go if everyone had a sword and some chain mail. Lee's Army of Northern Virginia needed everyone to carry a rifle, and also required wagons carrying millions of rounds of ammunition to be effective. It would need millions more after a few days of battle. Compared with a sword or a longbow, the Civil War rifle was an intricate piece of machinery that needed constant maintenance and was relatively easily destroyed and not so easy to replace. Furthermore, the soldiers and their support were transported on a network of ships and railroads, requiring maintenance and even expansion. The quartermaster and the logistics officer, heretofore minor players at best in war, now became decisively important individuals.
What also changed was the introduction of the mass conscription army. Wars were no longer fought between standing classes of professional soldiers (e.g. the Roman Army - the "combatants" for Augustine), but instead between huge numbers of young men forcibly conscripted from civilian life for the purpose. The point of all these young men was to be the delivery point for all that destructive energy manufactured by the nation. Thus the Civil War battle was largely a matter of rows of young conscripts facing each other, repeatedly executing a series of mechanical motions - just like a factory worker - load, aim, shoot, load, aim, shoot, load, aim shoot - until one of the rows of young men was destroyed. Or both. It wasn't Augustine's kind of war anymore, and the distinction between "combatants" and "innocent noncombatants" was disappearing. For in what way was the factory worker innocent that the poor Georgia boy taking a minie ball in the face wasn't?
And this was something that William T. Sherman understood. His March to the Sea (see Terrible Innocence: General Sherman at War for a perceptive account of this, or Victor Davis Hanson's The Soul of Battle: From Ancient Times to the Present Day, How Three Great Liberators Vanquished Tyranny) evidenced a brilliant understanding of what modern war was about, and also revealed a moral clarity missing from a lot of the armchair generals questioning the wisdom of Harry Truman. Rather than continue the practice of standing up rows of young men to mow each other down, Sherman marched through the South and destroyed the material foundation that kept the Confederacy in existence. His march caused a lot of suffering, yes. But the cost in human life was paltry compared to what was going on in Virginia in the attritional war between Lee and Grant.
Sherman understood that Southern civilians, especially the plantation owners, were in no way "innocent noncombatants." They were the ones who started the war, kept the war going, and insisted that the young men stay in their trenches at Petersburg and suffer. Here is Hanson quoting some of Shermans' soldiers addressing Southern women:
You in wild enthusiasm, urge young men to the battlefield where men are being killed by the thousands., while you stay at home and sing "Bonnie Blue Flag"; but you set up a howl when you see the Yankees down here getting your chickens. Many of your young men have told us that they are tired of war and would quit, but you women would shame them and drive them back.
Sherman did not restrict himself to destroying purely military targets. In total war, everything in the nation is put in the service of the war. A cornfield is just as necessary to the war effort as a cannon factory. So the cornfield was burnt.
And we come to what is missing in the analysis of James Akin and Dr. Feser. Akin writes of "dogs that didn't bark", but the real missing dog is the missing dogface - the 17 year old farmhand from Georgia, conscripted into the U.S. Army, and about to be sent into Japanese machine gun fire. This young Johnny Reb nowhere makes an appearance in the moral analysis of Akin/Feser. But it figured significantly in the mind of Harry Truman, and thank God for that.
The question facing Harry Truman was not the pristine academic one of killing or not killing the innocent. The tragedy of modern war is that the decision often boils down to which innocent lives will be taken. Will it be the Japanese civilians in Hiroshima, or the farm boys from Nebraska and Georgia who will be killed? Why is it a "more morally pure intention" to drag the kid off the farm, put a gun in his hands, and send him onto the exploding beaches of Kyushu, rather than nuke Japanese civilians? To raise this question is to answer it, which is why Johnny from Georgia is missing in action from the Akin/Feser argument. While Akin spends time making fine but pointless distinctions among Japanese targets (only those involving "war resources" are legitimate, when everything is a war resource in a modern total war), he has no time for a moral analysis of the American boys his thinking would inevitably send to their deaths.
Harry Truman was Commander-in-Chief of the U.S. Armed Forces. The unstated agreement between the C-in-C and the soldier is that young men (and now women) will put their lives in mortal danger under the President's orders; and that the President will not spend their lives unnecessarily. Truman would have violated his duty to every American serviceman if he had a way to end the war, but instead ordered his soldiers into battle in the name of a morally pure intention. Unfortunately, Truman did not have Sherman's option of destroying property rather than lives. Instead he ordered the nuking of Japanese civilians for the sake of saving his men; men who, in the modern fashion, were really just civilians temporarily in uniform. Yes, Truman ordered the deaths of innocent people; in doing so, he avoided ordering the deaths of innocent young American men. There is no way to stay clean in modern war. Just how would the armchair President's have stayed morally pure at the end of the war? This is another dog that never barks in Akin's argument.
I'm glad I served under President's Reagan and Bush Sr., and not Presidents Akin and Feser. I wouldn't want to serve under any President who would send me into machine gun fire for the sake of his moral purity.
And if this puts me out of line with the Catechism.... so be it. But I suspect Akin's interpretation of the CCC passages in question is not the only one.