You can look up the Nuremburg Principles as to why the prosecution took the actions they did. I think the motivation for the numerous death sentences and harsh punishments was due to the heinous nature of the crimes regardless of what superior orders were. It is generally held that a service member has a duty to refuse unlawful orders that are in violation of international law if there is a moral choice available to them. I know that the U.S. military requires all service members to refuse orders that are unlawful and they are held liable if they commit a crime under orders. The punishment may be lessened in light of the orders but that is not always the case. Most countries that abide by International Law, the Geneva Conventions and Law of War principles have similar standards.

*source: Nuremburg Principals, U.S. Law of War Manual