I bet $100 she knows, if for no other reason that thus far Marvel movies have been (loosely) using comic book storylines as the basis of their plotlines. M.J. found out about Peter/Spidey in both the Mavel and Ultimate continutities, though they found out in different ways.
I think you’re right as to the “Hey, wait a sec…” look on her face after kiss at the end of the movie as being foreshadowing.