John listened with a sinking heart because there had been a part of him that hoped he wouldn't hear the truth in Dean's words concerning Jo. John still considered Jo a part of the family, dating Dean or not, but he'd hoped, now that they were all as 'settled' in one place as they could be with people arriving and being taken away every day, that his son would find with someone what he'd found with Mary all those years ago. He'd hoped this break up wasn't the end, but he could hear it in the way Dean spoke. It wasn't just the words of a man trying to protect everyone by drawing back, it was the pained sound of defeat, Dean admitting his best hadn't been good enough for Jo, that it wasn't good enough for himself for Jo and there wasn't anything that could change it unless those changes were inside.
It wasn't the same, Dean's situation with Jo and John's with Mary, and John could that, had to see it to be able to help Dean. With him and Mary, there had been much more at stake, from years of marriage shared to knowing that they were meant to be together to him knowing what it was to lose her to both having lived, in their own ways, a torturous Hell. John would never compare them on terms of what they said about a person, because she was still warm and good and right, spirit for twenty plus years or not, and he'd become a monster in Hell, but they were the same in that they had both known suffering and come out of it needing each other more than ever, kindred spirits in experience, understanding how deep their love really was, even if John wasn't certain he had much capacity left at times to love her. She believed he did and some days he could believe it, and on the days he couldn't, he just believed in her instead. He had needed her, needed her so much he couldn't let go of her, and never would.
But Dean wasn't him, no matter how alike they often were, and it only told John even more than what Dean was fighting for was different than John. It was Ben that John had to keep him fighting for, not some lost ideal of love.
"That's not gonna happen, Dean," he said gruffly. Even now, John couldn't look at Ben Braeden without seeing the child Dean had been in a hundred little ways beyond the obvious that he was certain the others missed by not having known Dean or by seeing Dean through different eyes. But Dean and Ben, they were peas in a pod if there ever was two that illustrated that.
"But even were it to, you'll still take care of him, because he loves you and you love him." That was clear as day, even if John was reasonably sure neither of them had ever said as much to each other. "You want him to be yours and I'm pretty damned sure he wants you to be his Dad. If a damned paper says otherwise, it'll get thrown out and you two'll make your own future."