I would have been extremely hesitant to bomb civilians even if the Japanese and Germans deserved it. If there was any other way to use the bomb, say on military targets, that is what President Yarddog would have done.
Unfortunately dropping them on cities was probably the only option.
Japanese war production was spread throughout small workshops in their cities. Precision bombing of industrial targets was tried but found ineffective.
In March 1945 the USAAF began conventional fire bombing. The most destructive air raid of the war was the March 9 firebomb attack on Tokyo killing over 80,000. Atomic bomb casualty numbers include deaths occurring up to four months after the attack but for immediate lethality they were equalled by the firebombing campaign.
One bomb to turn the place into Dresden seems more efficient than sending thousands of planes to do it and lose thousands of Americans.
Like Dresden, the intention was to make the enemy lose their thirst for war.
It worked.