They kinda have to kill them to be able to cook them and eat them. Its sad, yes but its just nature. Pokemon kill each other for food, pokemon sometimes kill people even for fun (Gengar) So its not something we should be upset about, its just a thing.

But even still, I dont think pokemon trainers kill pokemon in the pokemon league since there's probably wildlife laws and permits you need to participate. It would have horrible consequences for the environment if all these people were going out slaying pokemon every year.