My thoughts are that he is wrong. If using the atomic bomb was wrong, so was the whole prosecution of WW2, in all theaters. War is bad ... but either it’s *all* bad, or it’s not. Weapons are just a tool.
If you will check the article, you'll see that it's neither the "atomic" aspect nor the "bomb" aspect that Jimmy Akin is objecting to per se. From the article,
"I am not a Euroweenie or a peacenik or a political liberal or even someone opposed to the use of nuclear weapons in principle. I can imagine scenarios in which their use would be justified."
His precise point is the one made by the Constitution on the Church in the Modern World, Gaudium et Spes, a major teaching document of the Second Vatican Council: that when the noncombatants constitute the target; when their deaths are part of the intended impact of the act; then their deaths are not justified as collateral damage.
He backs it up with this quote from the Catechism:
"Every act of war directed to the indiscriminate destruction of whole cities or vast areas with their inhabitants is a crime against God and man, which merits firm and unequivocal condemnation." The Link to the Catechism is well worth looking at for context.
It is not true that, war being bad, it's either "all" bad or it's not. The just use of military force, including lethal force, targetting military aggressors in order to force them to cease aggression, is a positive and honorable thing, however bloody it may be. It is not murder.
The unintended but foreseeable collateral deaths of civilians is likewise morally tolerable, if it is proportionate and not directly intended. (By way of analogy, this would be like the death of an unborn baby because of a doctor doing a hysterectomy on the mother's cancerous uterus.)
The intentional killing of noncombatants is murder. (Analogous to direct abortion.)
The difference between justified killing in war, and murder, is pretty well spelled out in the U.S. Army Field Manual. That's a traditional American military principle I consider essential to defend.
Where’s the condemnation of Japan for its sneak attack on Pearl Harbor?
I guess it depends some one which country is doing the attacking....