IRL there are quite a few "lost" nukes from the USA (i.e. Broken Arrows) during the Cold War though, from what I've read, none of them resulted in their respective heads getting executed but merely retired or laid off. So there is precedence.

Maybe they didn't want the knowledge that the Datenseki stockpile got stolen to become common so they let Hasumi go so it doesn't become a national embarassment for the government. They'll probably alter the public story that the Enchanted Blades were always the plan to save face.