Being a rated pilot before entering the Navy, I can totally relate to your story. I hear stories like this all the time, especially with second rate cargo companies. As far as that referal hurting you, I wouldn't worry too much about it. Like "ThisGuy" said, if you have five giving high praise about you will make them question the bad. If you really want to help yourself out, get letters from officers in the service now, or retired officers, friend's, family it doesn't matter. The people responsible for selection will like those kind of references better. If you can get one from a senator, your golden.