The Detective Pikachu movie is actually premised on the recognition that battling Pokémon against their will is unethical. It's kinda strange to have that as canon, when the entire rest of the franchise encourages you to battle them and the games provide zero alternative.

On the other hand... I think your concern here is just about the worst example of pearl-clutching over video game violence that I've seen. Kids don't have a problem sorting fact from fiction when capturing Pokémon involves throwing a ball at them and the Pokémon somehow becoming entrapped within.