Bombing is never pretty. I am not sure justified is the right word. Things happen in wars that no one wishes had happened. The purpose of bombing is to end a war faster. If there is no injury and death, or great destruction, wars will not end as quickly.
I do not think it is ever right to bomb innocent civilians in the name of war. Even looking back at Truman's decision to bomb Hiroshima and Nagasaki in the name of saving American lives was not a good choice. The American lives saved were lives of soldiers, not civilians.
It was either that or don't bomb at all, as precision bombing technology did not exist. So in effect you are asking was bombing justified? Was war justified?
Strategic bombing had a significant effect on the outcome of the war when all was said and done. It limited war production for Japan and Germany, disrupted transportation, destroyed resources and did much to hasten the end of the war.
It is a tragedy that civilians are killed at any time, and it is a tragedy of World War II. I cannot morally justify the killing of anyone in my mind, for any reason, but if I accept the premise that World War II was inevitable, and that the US would be in it, then I also have to accept the premise that civilians will die in large numbers as a result.
Up until the World Wars, when there were still "Rules of Warfare" in place, civilians were not supposed to be attacked. Of course, by the destructive process of war, rules go by the wayside. However, even during World War I fighting was mostly contained to opposing armies; the civilian bombings that did occur were very effective, but small in scope. Wholesale slaughter did not begin until WWII. As an example, during the Battle of Britain, the mutual bombing of airfields and military sites were the only intended targets. However, Britain "accidentally" (we're not sure) had bombs fall on Berlin at one point, and Germany retaliated by bombing London. The pervasive nature of WWII is such that by the time of that World War, the civilians, factories, and military facilities were all the same thing -- all designed to maintain an all out war, and therefore everything was a target. The same case can describe mainland Japan.
Civilians always die during a war. That is the nature of warfare. Bombing centers of civilian population during World War II should perhaps be considered in terms of offensive vs. defensive military action. Germany and Japan struck first in pursuing wars of aggression against other countries. Bombing civilians to win a war of aggression, the sole purpose of which is to gain political power and national wealth, is beyond justification. Bombing civilians while waging war to defend one's country after it has been attacked is justifiable--tragic, but justifiable.
Hiroshima and Nagasaki stand as the only nuclear attacks in world history, but they were last resorts to end the war without mounting a ground invasion of Japan. They were preceded by six months of conventional bombing that had failed to effect a Japanese surrender. The atomic bomb was dropped on Hiroshima first, but still Japan did not surrender. The second bomb was dropped on Nagasaki three days later, but the Japanese did not surrender until six days after that. Bringing to an end the war with Japan required the most extreme military action, clearly.
Was the United States justified in causing such horrendous damage and death to the civilian population of Japan? Stated another way, was the United States justified in using the most extreme means available to defend itself after having been attacked, when less extreme measures had failed to win victory? President Truman believed so. He chose to end the war and personally accept the judgment of history, whatever it might be.