I had a few ideas for someone who's family is tied with the enemy organization - so they were either born into it too, or at the very least their family benefited from their business. Either way, nowadays they've left it behind.
It might be fun if they thought of the organization as almost like family for a time, could lead to some fun emotional conflict later on. Maybe the reason they wanna go on the journey is to find themselves/get away from the past/make amends by helping Pokémon or something.