Arizona State University now offers a Master of Music in Music Theater Performance: Music Direction. It seems like a cool opportunity to learn by doing.
The only other degree I've found that's similar is at Shenandoah University, which offers a Bachelor of Music in Music Theatre Accompanying. The rest of the learning opportunities mainly take the form of 'internships', or brief workshops like the Goodspeed Opera House's Music Direction Intensive.
Another source of info:
Peter Hilliard's blog, Music Directing the School Musical