I recall a few animated flicks/series where the hero actually kills the villain.
In the 1983 animated feature 'Fire & Ice,' the mysterious and enigmatic hero Darkwolf put an end to the evil and powerful ice-prince Nekron with his battle-ax.
Jedi Knight Anakin Skywalker force-crushed the techno-union leader's breathing apparatus, effectively killing the separatist in the animated 'Clone Wars' series.
In 'JLU's' episode Panic in the Sky, Supergirl dispatched her clone Galatea permanently in a rather 'shocking' way (pun not intended) by using the watchtower's power conduit and thus saving her colleagues and the space station itself.
In the 'Legion of Superheroes' animated series, Imperiex met his timely demise at the hands of Brainiac-5, snatching away the opportunity from Superman-X.