To be clear, I'm not saying I think the Pac 12 would require the LDS Church to start accepting homosexuality as equal to heterosexuality in all respects, for example by marrying gays in the temple (or elsewhere). I think they would accept some degree of differentiation, based on historical religious beliefs.

But I don't think they will let BYU in as long as the Church continues some of the more far-reaching policies and practices in this area -- for example, not baptizing the children of gay couples, or actively and visibly campaigning against gay marriage (as with Prop 8). I think it's those high-profile, highly visible policies and actions that have drawn the ire of academia, much more so than our actual basic doctrine or theology in regards to homosexuality, which don't differ much from many other churches.