Dean had a slice of happiness and the darkness had still followed him. Still sought to pull him back down into that pit of evil and pain. He had Cas removed Lisa and Ben's memories of him to protect them, to allow them to move on despite it killing him. Destroying his bit of happiness and normal that they had provided to him when he desperately needed it.
"Dean..." Mary reached out and touched her son's face gently. "I'm sorry. I'm sorry you had lose them." Maybe it had been for the best, to protect them and Mary knew it, but knowing that it probably haunted Dean everyday destroyed her. It was just another rock added to the piles and piles he carried around with him; the world was always on his shoulders and his guilt always ate him alive.
Mary wrapped her arms around her son and held him. She knew there was nothing she could do to make it better; she knew there was nothing she could say to take away that burden. Ben being here and not knowing Dean and now Dean knowing Ben was his son? It was more stress. More fear. He didn't want to hurt Ben more than he had and he wasn't sure what would happen given Ben didn't remember Dean anyway.
"We don't know what happens when people get sent back. They may not remember ever being here in the first place," Mary said quietly. "Ben not remembering you makes it harder, but telling him is probably a good thing. we may be here for a long time and he's essentially alone. This way he'll know he has a family behind him, people who will fight to protect him no matter what." She kissed the top of his head lightly. "I know he would be so happy to have you as a dad, Dean."