I just saw this quite old post and could not help but comment. I too am a Moody Alum who has moved to a more progressive place (though mad props that you are still there and a progressive!) and applied to YDS for Fall 2011 (MAR-concentrated ethics). I am actually currently an MTS student at the Boston University School of Theology, and so applied to transfer to Yale. I did not find Moody to be a hindrance in getting into BU, which is a mainline Methodist seminary and quite liberal in orientation - in fact, I got a full ride and a stipend. I also, however have work experience and an MSW, so it is not the exact same situation, but I find that in many of these schools there is sort of an unspoken "evangelical affirmative action." In fact, YDS in their most recent brochure chose to highlight the evangelical student group. So take heart and say 'hi' to Mr. Milco for me. He is my fav.
Meanwhile, we can both fret about admission to YDS )
Sara