I wish everyone would take the small amount of time to realize that Gaga used the strongest metaphor possible to make a point. In this song (Judas), Jesus is depicted as the man who has always treated her right and has never done anything wrong, while Judas is another man whom she loves because he is so different than "Jesus". Everybody has had a struggle between two people; you can love both, but one pulls you in a little more. And that is what this song is about. Love. Choosing your own path and finding your own happiness in sorrow and excitement. It isn't directed toward Jesus and Judas directly. As stated above, it is the strongest way to get the message out there.
Do you all understand now?