You're right. It is their fault if they get turned on.

[ Snake narrows his eyes at her. ] The way you talk about them isn't going to make them want to protect you. It might be easy enough to boss around, say, a Totodile, but what about when it becomes a Feraligatr? Will it be so easy to boss it around then, call it worthless?

It's going to be hard for you to become a Pokemon Master if all of your Pokemon abandon you. Or you die.