So, according to this Deseret News article, the sports department knows of a little trick to get their athletes around Honor Code violations:
In past situations dealing with honor code issues, some BYU students, including athletes, in connection with counsel from an LDS Bishop, have withdrawn from school before the university's honor code office officially deals with their case and makes a determination on their standing as a student. In this regard, if that person receives a required ecclesiastical endorsement after one or two semesters, they can return to school without a university ruling on a non-academic issue.
BYU operates on a three-semester system. Missing spring and summer sessions is equal to a full fall or winter semester.
Just thought I'd pass the information along. It's not fair that the athletic department keeps their secret from everyone else.