This looks bad to people on the outside because they don't understand what membership means in the LDS church. They think it just sounds like someone deciding to attend a different church gets punished for their personal preferences.

But membership in the LDS faith isn't just about attending the church you like best. When you become a member you make solemn promises to God. We all fall short of those promises occasionally, that's what repentance is for. But when you go as far as to have your name removed and officially end your membership, then you are wholly repudiating the promises you have made to God.

So, yeah, hard to get an ecclesiastical endorsement.

To put it another way, BYU has a very unique mission (http://aims.byu.edu/). If you have your name removed, then I think by definition you are saying you no longer share that mission.