A lot of non-Germans would have suffered if a nuke was exploded over Berlin. That alone made it a non-starter.
If the bomb had been ready, they would have nuked Germany.
The Allies turned Dresden into a firestorm knowing full well there were Allied POW’s in the city. That didn't change the target selection.
If you read what men like Harris and LeMay wrote, they knew that they will killing on combatants. LeMay sacrificed many, many aircrews in daylight bomb raids to limit that. It was factored into part of the cost.