I don't really know much about the early series, but I never saw a Pokémon die in the Manga before. Remember when Koga's Arbok got sliced in half? That specific one was able to escape from being dead by regenerating itself, as long as the head isn't off. Team Rocket may steal and do evil experiments on the Pokémon, and sometimes they do kill Pokémon, but they never actually show the actual killing on the page.