I have a degree in economics from BYU and an MBA from Dartmouth. I have found that my degree from BYU has always been viewed as much more similar to an Ivy League school than it has to a traditional state college.
Part of what I hear you saying is that there are a disproportionate amount of highly qualified students from BYU and that they can't all be accepted in medical school.
Before you assume it is some sort of discrimination, I would like to see how many students from BYU apply to med school relative to other schools. My hunch is that there are far more students as a % of the BYU population that apply for Ned school than at other schools. Too much supply for the demand out there.
Med School at the U has always been a high hurdle for BYU grads. Nothing new there.