It worked for me. Stan loved the Jennings family, and Stan had acted on his emotions vs complete loyalty to his job in the past. He did it with Nina and Oleg. His connection with the Jennings ran much deeper than that of Nina and Oleg. The confrontation in the garage was such a mix of emotions. Stan's angry interrogating words turned to words of emotional hurt once Philip took off his mask and released confessions of his true self. I think Stan felt Philips pain of having to abandon his son as a consequence of serving his country. That loss is greater than going to prison. Philip and Stan both felt guilt about their work and questioned the validity of it in the past, causing both to leave it (P being a full time travel agent and Stan moving to the crime unit), but only to be sucked back in. I remember Stan telling Renee he was thinking about quitting the FBI, because it felt $hitty and he was tired of feeling that way. During Stan's and Philip's exchange, you could tell that Philip too was sad about the end of their friendship. All the actor's did such a great job with their facial expressions and body language. That has been the case throughout this series. Anyway, I think in the end what finally swayed Stan the most was when they asked him to take care of Henry. Stan has always had a nurturing nature about him, and he was like a second dad to Henry. Them asking and trusting him to take care of their kid struck at a cord with Stan. Through all the betrayals and lies, there was genuine love. Maybe if the FBI ever got that message decoded it would give Stan some peace knowing that P & E were telling the truth about it, and they were acting on the right side of the law (as was Oleg).