I think that part of the problem with this idea is that a lot of times the Musical Director of a show is also the person who has done the Orchestrations, which IS a Tony eligible category. So you would have a bunch of people who were up for Tony's in 2 categories. Someone please correct me if I'm wrong.
I do think there should be a Tony for Best Ensemble though, and I don't mean the Best Chorus. I mean the Best overall Cast of a production that includes everyone in it.
"If you've got something to say, say it, and think well of yourself while you're learning to say it better." - David Mamet