Look, Archie never said he was happy with what Gold did, just that he thought that the punishment went too far. (Though some sick part of him hadn't been too torn up about Hook. Getting tortured for information in a ship's hold for days on end with no hope of rescue since everyone thinks you're dead doesn't sweeten one's temper towards the one doing the torture.)

"You're welcome," Archie said with a small chuckle, closing his jacket back up as the nurse entered to finally give Gold the okay to leave.