First, there must be some basic assumptions described and some basic questions to ask before continuing into my theories.
What is the purpose of the BYU Honor Code? I believe that the BYU Honor Code Office exists not only to help enforce the Honor Code but to assist in creating a community of students particularly homogenous morally. By achieving this, it destroys most discussions that would take place on a typical college campus. It also works to create dependence upon the university and to create an atmosphere of obedience and (for some students) fear in the face of disobedience. But I believe the reason the BYU Honor Code exists is to provide an atmosphere wherein the Church's PR machine can actively promote the Mormon lifestyle and ideas to the world at large.
Does the Honor Code particularly despise or dislike gay BYU students? I do not believe so. I don't think that the HCO staff dislikes anyone so long as they don't upset the carefully created atmosphere at BYU. If the gays toe the line, the HCO is fine. They do not care one way or another about gays, in my opinion. They are not there to provide true counsel or help students achieve a higher level of understanding about the Gospel or complex moral situations. They are simply the foot soldiers of the BYU PR machine.
So why hasn't the HCO acted against USGA? I think the HCO is being held back from doing so in this climate of heightened awareness and favor for LGBT causes. The high profile involvement of the LDS Church in Prop 8 has not been forgotten. The ongoing PR efforts of the LDS Church to cast themselves in a kindlier light has bound the hands of the HCO. The HCO can't be seen attacking nice gay kids. That would be a horrendous scandal on the Morg and BYU's hands. No. Rather, they are being forced to wait.
Another thing to consider is this: USGA offers the HCO the golden opportunity. Prior to USGA's existence, the HCO had to be hyper vigilant about the activities of those bad gays. They had to seek out a minority that could practically be invisible amidst the student population. USGA has members proudly proclaiming their sexuality for the whole world to know. Take a casual stroll through USGA's meetings and after social gatherings and one could easily assimilate information about which members are in same-sex relationships. Pry a little further and knowledge of those intimiate aspects of the relationship will be known. It isn't hard. USGA is full of friendly and happy kids. They aren't afraid of the HCO, ironically. The HCO's silence has emboldened the students of USGA and created a little utopian world where the gays can live in peace and harmony. All the HCO has to do is sit and wait for the USGA group to become louder and more pronounced about their lives and their relationships.
Also, the longer the HCO waits, the more politically active USGA becomes. The USGA is becoming more activist in their activities, a normally good and typical thing. But BYU's obsession with political neutrality creates a potentially tense situation for USGA. The more it creates a climate of activism, the more the HCO can document and create a long list of violations USGA has done. USGA's unique situation of not being officially recognized on campus means that they don't have to follow the neutrality requirement of BYU's clubs. However, this doesn't shelter them either for there is no legal or bureaucratic protection for USGA. Should the BYU administration or the HCO ban USGA from campus, there is no recourse. USGA stands vulnerable to the favorability of their message to the administration and powers that be on campus.
Essentially, I propose that the HCO waits to act because they don't have to research that extensively. If they are smart individuals, and I assume they are, they just have to wait for USGA to mess up. And it will. The desire for freedom is too tempting a prize to avoid. How could you not want to be treated equally? And that is where the HCO lies in wait. USGA members at BYU forget that while the HCO does not hate or dislike gay students, they also do not see them as equal to their heterosexual counterparts.