I would then offer the dad the possibility to maybe do a dual enrolment so that the girl could still be enriched and yet still be able to live as a normal little girl with her peers.
I agree with you here. The movie didn't at all focus on how Mary did in other subjects, so we the viewers can only assume that she only excelled at math. If this is the case, I feel like the situation at the end of the movie, where she was taking dual-enrollment classes for mathematics exclusively like you described in your assessment was the best course of action, as it did have the best of both worlds, where she was finally intellectually challenged while still getting to participate in normal girl activities.