Why did the secretary of war think the use of atomic bomb on Hiroshima and Nagasaki was a terrible think to do but better than any alternative

During WWII, the soldiers of Japan had a philosophy. It is called Bushido - they would rather have all died than surrender. The secretary of war realized that more and more people would die (millions more), because they would always refuse to surrender and fight to their last breaths. So, his reasoning was that it was better to kill a few hundred thousand people rather than let the war linger on, killing millions more.