There is a line between a sitcom's lead character (even in an ensemble like Wings) being 'long-suffering', which is needed for them to be the lead, and them becoming an unfunny doormat. I've always felt that Joe fell into this in the middle of the show's run, and I see this episode as the starting point.
First, how is the burden upon Joe to grant forgiveness? What this lady wants, she has to earn back. How does she do this? By commenting that he was 'tight-cheeked even in the womb'. Great, Mom. Joke with your moral clone Brian and Helen 'I Just Gotta BackStab My Man' about the worst thing you ever did. This would be acceptable as nerves overriding her common sense, if, after Joe's memorable calling-out over exactly why he's so super-serious, she hadn't dodged by revealing the huge secret that...she's just not much of a mother. In other shocking news, Wings had similarities to Cheers. In this one instance, Joe is right, he is unequivocally right, beyond the ability of false friends and random strangers to change that. But the writers have him give that up for a vague assurance that she didn't leave because of a bad school project of his. The problem is not that he forgave someone he loved who wronged him. The problem is that by doing it the way he did, every waiter/politician/customer/whatever with attitude for the rest of the series can now walk over him--and most do. It set the wrong tone for a character who could have had his moment before going back to the usual lot of a sitcom lead.