What I find interesting about that last scene is how Dean will react to this new perspective on his Mom because its undoubtably going to change.
As mentioned in previous episodes the boys have come to accept that although their Dad’s way of raising them would not in any way win him Father of the Year, they do still appreciate the fact that he was there majority of the time.
And that’s what’s probably going to kill Dean the most.
In his childhood I have no doubt in my mind that Dean would’ve had those same thoughts about his Father’s raising of them and I can imagine that he would repeat over and over to himself about how Mom would have looked after them, Mom wouldn’t have left them, Mom would’ve been back for Christmas, because that was his fantasy. His perfect ideal. It was his brain keeping the memories he had of his Mom alive through how he thought he remembered her.
But now that’s changed.
Now, Mary is the one to have left, and in my opinion, her reasoning is nowhere near as sound as John’s. John didn’t want to be away from his sons, but he needed to find the thing that killed his wife while also killing monsters to protect his boys. Now in no way am I saying John was a saint, but we know that at the end of every hunt he would come home to his boys and take them off with him.
They would be together.
And for all of his flaws, John Winchester had family at heart and he loved those boys so fucking much.
Dean knows this, and regardless of how much or how little resent he holds for his Father now in later life, he loves his Dad too, and always will.
It’s going to be hard for him because of all the people in his life, he never expected his Mother to be the one that walked out on him and Sammy, he would always have guessed that to have been their Dad.
But John never did.