Personally - I don't think the Brethren give a lot of thought to BYU until/unless there is negative press. There may be a bigger element of BYU admin trying to read their minds and do what they'd like than there is the Brethren actually giving specific direction about some things.
While I don't necessarily see the honor code as a detractor - I don't think we can deny that the honor code makes the recruiting pool smaller for BYU. There are some relatively good dudes and good players who don't want to commit to never drinking while in college, never having sex while in college, never having coffee while in college, always cutting their hair and shaving while in college, not wearing shorts or flip flops to classes...etc., etc., etc....