Today, we condemn nations that use weapons of mass destruction in war, therefore it would be hypocritical not to use the same standard.
If we think of WWII Japan as individuals rather than as a collective entity, there were likely many individuals, especially children, who were innocent. Why was it okay to kill those children? Why do we condemn the deaths of children in war today and not those deaths?
Even the soldiers were captives of a concept as it were, in following their Emperor. They were misled. Once they were no longer misled, it turned out they were as decent human beings as anyone else.