I don't think that BYU can keep things under the rug anymore like they did 30 years ago.
In just 10 years the social media has transformed things. With facebook, twitter, cellphones that can take pictures and movies, etc it's very difficult to keep things secret.
BYU isn't as slow on these things anymore. Maybe it's because they're a more recognizable university than before? Maybe it's from pressure from the LDS church? Different leadership at BYU? But, I think Davies was a good example of this. BYU easily could have waited a few weeks to "think about" and debate what his punishment should have been... During this process, he and Jimmer could have led BYU to a much higher seed or further in the tournament.
The system isn't perfect and I'm sure honor code violations happen all the time (and don't go reported). But I'm pretty sure if you break a biggie, like having sex, it's going to come out and they will be punished.