Agreed Tony. My main emphasis would be (assuming this is a real game that counts on the books, not a scrimmage), once you got this varsity coach to fill in as a ref, he is now a ref not a trainee or some sub-species of ref. (I know that when he coaches, he is a subspecies of the human race!) As a ref, he is your partner, and deserves the same treatment any other partner would get. To do less will damage the credibility of both partners and make the game worse.
And I also took issue with what I read to be criticism of a coach for raising an issue, when I bleieve that the problem resulted from the ref's handling of the situation. And you know I don't default to siding with coaches.