It's something of a stretch to call him an apparent asshole. More like a usually decent person who'd flake out sometimes. But the thing that bothers me about her knowing is that Mary Jane goes from the woman who loved Peter Parker for his own sake to the woman who knew he was Spider-Man, so maybe she would have loved him if he weren't and maybe she wouldn't have.
That's the same reason I don't buy the "Superman is who he really is and Clark Kent is the disguise" school of thought. Clark Kent is the way Kal-el relates to people as people and has them relate to him in the same way. As Superman it's always, to some degree, a hero and an awestruck potential victim.