I am sure the brethren are guided to a degree in relation to BYU, but I don't think it all is. At least it is hard for me to believe that. Unlike the church's organization, BYU's organization isn't perfect. And it doesn't have to be.
But yeah, the honor code needs to be changed dramatically. Bishops should handle ecclesiastical endorsements and that should be that. Students should sign the honor code but there shouldn't be policing of it. It seems too much like the pharisees and I have are hard time thinking that was set up via revelation.