Alicia Morton was definitely an Equity finalist. Alicia was either already in "Les Miz" or got "Les Miz" shortly after the "Annie" auditions. Both Andrea Bowen (who is playing Molly while Alexandra Kiesman is singing "Maybe" on "Turning Point") and Alexis Kalehoff got "Les Miz" a couple of weeks after "Annie" auditions were over. Andrea Bowen was only 6 at the time and was the youngest actress to play Young Cosette on Broadway. All 3 girls were in the cast when Ricky Martin was Marius.
Regarding the other finalists, I am sure there is a ton of "Turning Point" footage that hit the cutting room floor. I definitely believe that part about pressure to choose someone from the open call because of the publicity with having Andrea there and everything but I think Martin et al. could have chosen whoever they wanted from the open call, right? Joanna was featured prominently on "Turning Point" BECAUSE she got the role...they probably shot footage of all of the contenders and would have edited according to whoever ended up getting cast. The biggest problem, besides not really being able to choose an Equity candidate, seemed to be that they weren't 100% satisfied with any of the finalists but were under time pressure because of the TV special to make their decision then and there. Without "Turning Point" perhaps they could held more extensive auditions and found somebody they loved. I never got the impression from the way "Turning Point" was edited that anybody except maybe Martin really loved Joanna.