That's not really a good example. The options were invade, and millions of Japanese civilians die along with solders on both sides. The other was to use a weapon of mass destruction to try and make Japan capitulate. The bomb was the more merciful, and least bloody route.
A better comparison would be the time we bombed that hospital in Iraq. Was any target worth it? The question really being asked, even by CNN, is "Is there ever a Hamas target worth that many Palestinian lives?"
I couldn't answer that. I would say that if it was something that could bring about the end of the hosilities and it causes Hamas to capitulate, then it might be a valid comparison. It could potentially save the lives of more people in the long run.
But, we're in the middle of this. History is being written as we speak, and it might be viewed differently in hindsight.
I will say that Hamas' propensity to put civilians in harm's way by literally hiding behind civilians really complicates the decision making.