@SerendipityJane
Returning to Heydrich - did he personally kill anyone who wasn't a soldier in war ? Yes, he may have been a legitimate military target.
Afaik he was leading nazi secret services, crystal night, lead the conference for "final solution of Jewish question" and more, which made him a war criminal responsible for deaths of millions before he even got to the post in the Protectorate.
Looking only on the Protectorate part, it's tricky.
He was tasked to focus on resistance fighters. Afaik the first thing he did in the function was to imprison and charge with treason the prime minister (sentenced to death and executed later), who was a Czech army general actually working for the resistance. Resistance weren't soldiers in the sense of organised army, but many wouldn't classify as civilians either. (I'm oversimplifying now, holocaust, martial law, ...)
Anyway, he was targeted more for political reasons (Czech position in international politics and post-war arrangements) than the evil things he did personally with his hands.