All the bombing targets were specifically chosen because they had significant military value. Hiroshima was the headquarters of 2nd Army. It had significant barracks, weapons depots, and was a major army communication center. Nagasaki was a major military port and weapons manufacturing center. These were normal valid targets under the rules of war at the time.

Sadly the rules of war allowed the bombing of civilians as long as there was military value in the bombing. By 1945 this included what was euphemistically called "dehousing," that is disrupting factory production by removing workers' houses. Nominally this wasn't targeting the workers themselves, but when you bomb someone's house and create a firestorm in the middle of the night, there's a good chance you'll kill the worker who lives there as well. So regardless of euphemism, the Allies deliberately targeted civilians.

When the Allies began bombing Japan Hiroshima, Nagasaki, and the other target cities were removed from the conventional bombing lists. They were basically preserved so that if they had atomic weapons dropped on them, the full effect could be observed. Had atomic weapons not been developed, the cities would have been bombed and many (most, maybe all) of the people killed in the atomic blasts would have died in firebomb raids instead. It is telling that Tokyo, Hamburg, and Dresden may have all suffered more deadly attacks than Hiroshima or Nagaskai. The atomic bombs were more efficient and quicker, but they weren't deadlier than the largest conventional raids. Conventional bombs killed far more civilians than the two atomic bombs did.

During the post-war trials (Nuremberg and Tokyo) some of the defendants tried to use the defense that nothing they did compared to the bombings. The prosecutors pointed out that bombings of civilians was an accepted part of war and that both the Allies and the Azis did it, so no one could base a defense around that. The legal argument was it was legal, regardless of how horrific it may have been. With such an argument, no one on either side faced trial solely due to the bombing of civilians.