DisneyGeek posted photos from last week's Fantasmic show and the characters appeared on Tom Sawyer Island for the finale. So it looks like at this stage in the refurb, the Mark Twain is not going to be used in Fantasmic.
In terms of the package, I think it depends on each guest. Having seen the show with the Mark Twain, I would probably opt to wait until it's back in the show before going to the dessert party. However, if you've never seen the show, then it might still be worth it to get the package because the rest of the show (including my favorite sequence: Peter Pan) is the same.