The World's Most Dangerous Idea, which is not only concerned about the immorality of our use of those weapons against Japan, but it is also concerned about the fact that a large majority of Americans have thought it was the right thing to do. The idea that there are certain "ends" (such as victory in the war with Japan) that can justify the "means" of killing innocent people has continued to this day to the justification of abortion and euthanasia.
Catholic moral theology tends to be more clear and uncompromising on these types of issues than what most people are used to thinking. There is another aspect of Catholicism that is probably even more foreign to most people, and that is the idea of redemptive suffering. Although most Christians believe that Jesus suffered on the cross to accomplish human redemption, most Protestants do not embrace the idea that the suffering of Christians can have a part to play in redemption. The Bible passage that most clearly illustrates this is Colossians 1:24, "Now I rejoice in my sufferings for your sake, and in my flesh I am filling up what is lacking in Christ’s afflictions for the sake of his body, that is, the church..." (ESV). I found the long article, 'The Catholic Holocaust of Nagasaki—"Why, Lord?"' to be a beautiful story of how redemptive suffering transformed lives in the aftermath of the bombing of Nagasaki, which was the most Catholic city of Japan.
Finally, I just read Sandro Magister's column called 'Why Christianity Is "Foreign" to Japan,' which includes an essay by Kagefumi Ueno, the Japanese ambassador to the Holy See, on the differences in Japanese and Western approaches to religion. The essay is very informative and shows some real differences in belief. However, it appears to me that some of the perceived differences are more a reflection of Western culture than actual essential Christian doctrine, which gives me hope that a presentation of the Catholic faith, properly inculturated, would have more traction in Japan, as it seemed to have in the days of St. Francis Xavier.