I was once like the OP's friend. I had low self-esteem so if someone insulted me I might protest but would give in at the slightest protestation, so I would say it was OK and then just continue on. Once I gained self-esteem I realized that these previous situations weren't actually addressed. Unfortunately in two separate situations it didn't work out well. In one the person's response made me realize that they really didn't care how I felt about anything they said, no matter how hurtful, so I've given them the cut direct. In the other, I think I was a bit too forceful and drove the person away.
If he did indeed just ask you why you said those things, I don't think he was rude. You could have been a bit more empathetic and asked him if those issues were still bothering him after all this time and what you could do to help. Or, since he was leaving, bean dipping and avoiding him was definitely an option.