Actually, the fireworks are after the first showing (9 pm, withe fireworks at 9:25); and yes, the do let you stay for them. They even let us in early for the second showing of Fantasmic (preferred seating) to see them, which was nice.
While you hear the music and see the shells, you don't see them as part of a coherent story (which relies on the castle). You still see Tink fly, and you see just how far apart the shells are really launched from. It is a lot of fun, though. I'd recommend seeing the fireworks from the Hub on another night if you do the Fantasmic seating, preferably prior to your Fantasmic seating (just to see what the show is supposed to be).
Dirk