Killing a hero is not impossible on a purely technical level. You could blackmail him, take a comrade hostage, or exploit some other weakness or 'kryptonite'. Furthermore, killing a hero can be beneficial - eliminating the hero of an enemy country, for example.
The problem is that lazy Japanese authors never think that deeply. They never analyze their simplistic tropes, and they never explore the possibilities. They show no concern for maintaining suspension of disbelief, and they never improve, and I don't know why. Maybe because they never receive much-needed criticism, especially from professional writers. Light novels are called 'light' for a reason, I guess.
