From your OP, it sounds as if he has finished Uni now, but that this is hanging over him, and that must worry you.
Although this sounds rather a first world problem, and it's simple to say that he should give his head a wobble, he may, if he's not careful, let this affect the way that he feels about himself, moving forward in life. As a loving mum, you may want to remind him that you can't change the past, but warn him that feeling resentful can be incredibly damaging, leaving you forever wondering 'What if', rather than committing to life and making the most of it.
I get the thing about not fitting in with your peers. I went to an ordinary comp, but was always perceived as a bit posh, because I didnt have a local accent. I had a great time at Uni socially, but really struggled to find my niche when I left. I lost a lot of confidence, and clearly remember that feeling of "If I'd gone to a different school/Uni/whatever . . . " It gnaws away at you.
In a similar way, my Mum lost her own mother in her early twenties, which was, of course, incredibly sad. However, I remember becoming aware as I was growing up, that she was letting that one event, however huge, define her as a person. It was behind all of her decision making, all of her life choices, which is quite sad.
If your son is serious about this, listen to him. Let him know that his feelings are real, and that you understand. Obviously you can't change the past, but you can hear him out without criticising him for feeling as he does. Sometimes that's all that is needed, for him to get it off his chest and to start to build a life for himself. If it isn't enough, encourage him to get some counselling so that he doesn't hold off making the most of life and of his talents, by dwelling on what can't be changed.