It is only from knowing his wife so well, that Arthur sees the signs of Joan's thoughts. He wonders what could have happened between his time and his wife's. A thought he never thought that he'd have, but something clearly did for her to doubt their loyalty to her. Arthur knows that they would protect Joan long before they would him away from their world when his being their superior didn't matter.

"I will trust your gut instinct over anyone's, even a file full of documented information. I wouldn't give Annie and Auggie an option, but let them know that you are contemplating it. More of a surgical strike to give them a heads up rather than soliciting their opinion." Because while their lives will be affected, in the end the final decision was Joan's.