The craziest thing is she actually doesn't mind.
While to be honest she does, not every mother wants to look down and see her two sons together..in that way. But then again, the fact that their together is what brings her peace.
See the thing is, that while Mary may be dead, she can still feel her sons pleasure and pain. She knows when their hurt or when they're happy. So she also knows the only times they're truly happy is when their together.
She remembers those horrible Standford days. If she hadn't already been dead she might have died from all of Dean's angst.
But then Sam came back, and then everything made sense again. She remembers feeling the world from her oldest son's point of view. She could feel the anxiety over her husband, their father, the worry over their hunting, the jealousy/sorrow concerning Jess, but mostly his only emotions were of pure love. He was with his brother again, nothing else really mattered beyond that simple fact.
Strangely enough Sam had the excate same feelings.
It made her grin how much they were alike.
She watched from the heavens as her boys fell in love, and she's proud. She knows the world would be disgusted, and she also knows she probably won't be seeing her sons because of their choices. But that doesn't matter, because no matter where they go they'll be together.
And that's why she doesn't mind. Because they love each so deeply, it's impossible to reject.
Plus...they're her boys.