One can only assume the best of intentions. The desire to make Brigham Young University (BYU) a safe, friendly, professional, and faith-promoting environment for students is admirable. However, the current formulation of the BYU Honor Code results in an inappropriate mix of religion and academics which is damaging to and prejudiced against BYU's own Latter-day Saint students (abbreviated LDS, commonly known as "Mormons"). The Honor Code is counterproductive to its own purposes and goes against the spirit of the LDS faith.
The Honor Code currently states:
Students are required to be in good Honor Code standing to be admitted to, continue enrollment at, and graduate from BYU. In conjunction with this requirement, all... students are required to obtain a Continuing Student Ecclesiastical Endorsement for each new academic year.The requirements for obtaining an ecclesiastical endorsement are generous and flexible for non-LDS students, who are provided with three options:
Non-LDS students are to be endorsed by (1) the local ecclesiastical leader if the student is an active member of the congregation, (2) the bishop of the LDS ward in which they currently reside, or (3) the nondenominational BYU chaplain.Once baptized LDS, however, a student no longer has the option of receiving an ecclesiastical endorsement from the nondenominational BYU chaplain, nor from activity in a non-LDS congregation. LDS students are left with one option.
LDS students may be endorsed only by the bishop of the ward (1) in which they live and (2) that holds their current Church membership record.Finally, if the LDS student chooses or is forced to leave the LDS faith, they have no option and are kicked out of BYU.
Former LDS students are not eligible to receive an ecclesiastical endorsementThough BYU is typically welcoming of those of non-LDS faiths, it is unusually hostile towards LDS students, and imposes special restrictions on them to prevent them from leaving that religion. Presumably, it is the best interests of the remainder of the LDS student body that motivate this section of the Honor Code: it is an attempt to shelter them from doubt and dissent by weeding out "problem students." Its effect is, at first blush, in line with the Honor Code's goals. It censors dissent, creating a calmer environment.
But consider those students who might wish to leave the LDS Church. Surely none intend to do so upon enrollment at BYU. They fully agree to the Honor Code; as faithful LDS Church members at the time, or as converts to the faith during their studentship, these restrictions seem irrelevant. However, at some point, doubt sets in, and a decision is made to depart from the faith. Rather than go through the pains of transferring schools, many instead choose to simply slog through. They must live a lie for the sake of their academic career. The Honor Code manipulates behaviors by threat of academic consequences. If the goal is religious retention, then the effect is just the opposite: jaded graduates come to despise the LDS Church and BYU for causing them to prolong a pretense of belief. BYU offers no way for a member of the LDS faith to leave the church and retain studentship: this very case is explicitly prohibited by the Honor Code!
It is unbecoming of an academic institution to suppress or hide dissenting views. Worse, it is hypocritical for a religious institution to preach, "let [all men] worship how, where, or what they may," but then threaten academic consequences if an LDS student's conscience dictates a different form of worship.
In summary, the BYU Honor Code has the mere effect of improving the appearance of conformity at BYU, at the great cost of undermining the religious freedoms of its LDS students. Like a bad gang, the Honor Code attempts to maintain LDS membership by threat of punishment for leaving. The effects of this particular policy work against the Honor Code's true goals, and the spirit of this policy is in plain opposition to the articles of the LDS faith.
 BYU Honor Code. http://saas.byu.edu/catalog/2012-2013ucat/GeneralInfo/HonorCode.php
 11th Article of Faith. http://mormon.org/articles-of-faith