I didn't see Judas as so much a villain in JCS as misguided. I think the High Priest was written as more of a villain than Judas or Herod or the Romans, which is why Jewish groups reacted with such horror to the show. I remember my rabbi flipping out over the portrayal of the High Priest as telling Judas, "I don't know why you're filled with remorse." (Of course, the High Priest also said, "What you have done will be the saving of Israel," so there was SOME nuance, but not much).
In any event, Jewish people often respond negatively to JCS in my view because of the High Priest's portrayal as an arch-villain.
You alone can make my song take flight.