To be quite honest, this is the second time John encounters another probable killer who killed someone who was loved. We know he didn't kill Jessica's murderer, and he still got that other abuser in jail back in S1, and while they did deserve it, he never once thought revenge was wrong in that case, since he was sure they were guilty. So he never had to question himself on it. And we had never seen Fusco's viewpoint on preventing someone from killing another probably guilty person (I think).
But could they know in this case? John was almost positive that the guy was the killer, but Finch's experience taught him that taking revenge on someone who you think is the most responsible could be wrong, as he was with Alicia Corwin, which made him doubt of the man's verdict. This in turn made John think of his own actions: did he face grief at all? Or did he just take justice on his own and try to forget it ever happened? When Finch confronted him with this, he realized he had never really done the entire grieving process of Jessica's death, Carter's (as was seen in the Devil's Share) and Shaw's disappearance.
In conclusion, I wouldn't say it was a regression of their characters, but rather a bit of a closure on something that motivated the characters to be back when the series started, but we hadn't really see until now. I know that it would be awesome to have every single episode to be as awesome as Season 3's, but they started ramping up with the last 3 or 4 episodes. These are fine too, they can't really forget what they started for, and not every number is a "save him/her to save humanity from Samaritan" case.