I don't agree with the moral standard that as long as Iowa can't be occupied by enemies, we can just turn a blind eye to evil.
Without the complete submission and military occupation of Japan, they had the ability to regroup and re-militarize, and again in the future threaten American citizens and American interests in Hawaii, Guam, Australia, Philippines.
Japan was a dangerous and militaristic nation which had spent the previous 70 years attacking and occupying nations throughout the Pacific Rim.
Our intent was to force Japan to surrender unconditionally, accept a military occupation, and be re-made by us as a pacifist and non-threatening democracy.
We succeeded beyond our widest hopes, as Japan is now a democracy, a close American ally, and is constrained by it's American-drafted constitution from having a powerful military footprint.
So, you have to say in hindsight, Truman made the right decisions in the grand scheme of things.