Wars have long included the killing of civilians. During WWI, the Germans hoped to starve England of foodstuffs and war material by sinking ships using U-Boats. Even before that, Britain sought to starve the Central Powers using the British navy to blockade European ports. The British were so successful that by 1917 there were food riots in Vienna as well as German cities. Worse, the British maintained the blockade even after the armistice, causing more deaths in Germany, until the new democratic government signed the Versailles Diktat treaty.
FDR was willing to sacrifice 1,000 Americans at Pearl Harbour. The History Channel interviewed some of those who had deciphered the Jap code. The US knew the Japs were on the Way to Pearl, but FDR preferred surprise, and American entry into WW 2 as a united country.
During WWII the Allies bombed Hamburg and Dresden. More civilians were killed in the fire-bombing of those cities than in the A Bomb over Nagasaki.
Truman rightly used the ABombs on Hiroshima and Nagasaki - the bombs saved lives. Had the war not concluded, the US would have had to invade the Jap home islands. Not only would that have resulted in the deaths of thousands of American and Japanese soldiers, but the Japs would have also ordered extermination of western POW's and Western civilians interned in their camps.
Pacifists may decry the killing of civilians. But those engaged in war have long practiced such killing (even if they verbally criticize the practice.
Herbert Aptheker, the American Communist theoretician, once reportedly declared: "If the end does not justify the means, then what does?" Camus and others have noted how an end that is ever distant can be used to justify anything, and everything. Yet the innate pragmatism of people in most lands has permitted not only wars, but wars against civilians.