Only when the offense is so serious, or the pattern is so egregious does it ever effect a player's eligibility...and if it does, they are no longer allowed to be BYU students.
It should be the same with every student regardless of their talent. Joe Schmoe from Payson that's in computer science should be under the same guidelines as Brandon Davies who has NBA potential. Their challenges are handled by their clergy IAW guidelines that are established and given to the eccesiastical leaders. Once they lose the endorsement, they don't go to school, and they don't play. But no one ever has to know why...not even the coaches unless the player agrees to bring them in for support.
Now that could be tough on BYU coaches. Out of the blue a player that has been working through multiple problems...but who has chosen to not have them be made aware...could just go away. But that keeps it all between the clergy and the person. IMHO, that is the way it should be.