I can't imagine that John knew about Mary's deal with the YED, but I wonder if he figured out, later on, that she was a hunter. If you look at kroki_refur's episode review of doom (http://kroki-refur.livejournal.com/234806.html#cutid1) for this week, about halfway down she has screenshots of the journal entries John made about people visited by the demon. And if he knew about Mary's friend, surely he put two and two together about the mysterious deaths of her parents on the same day?

I agree with you about Sam and Dean ignoring both sides and finding their own way out of it. Brothers v. cosmos; I know who I'm rooting for.