There aren't enough graduate programs and the academic world wouldn't be cool with a religious school rising to that level. Academically the highest BYU can ever achieve is like unto a B10 school (but I doubt that ever happens). BYU is different and is meant to be different. I would love for more and more people to have the full BYU experience (and the OP helps to get people to provo). If you worry about rankings and perceptions I would pimp that Ivy league degree you have, not your undergrad. I will say I'm sure BYU's reputation, along with your hard work did help you get where you are.