"Are they going to use the Protestant Bible or the Catholic Bible?"
More importantly what are they going to do when some other religion wants to set up their own elective class - like Bhagavad Gita study, or Talmud study, or get-naked-and-worship-the-trees study. (Actually, that last might be very popular - leading to an explosion of Wicca).
It's one thing to survive a court challenge to voluntary Bible study. It's another to survive an establishment clause challenge when the issue is other religions coming in. In fact, I wonder if this is they very reason why the ACLU is standing outside the fray right now.
If I were the legal director for the ACLU (perish the thought, I'd have to take a pay cut for that job), that's about what I would do. Rent some students to request a Hindu study course. You could even include yoga and sell it as a PE credit. Then if the district refuses, bring an establishment clause suit. That way, you don't argue separation of church and state, you argue that a preference is being given to Christianity.
I would have no problem if there were a scholarly study of Bhagavad Gita study, or Talmud study, or get-naked-and-worship-the-trees study (Wicca).....one hard part would be getting enough student interest -- and another hard part would be having a scholarly study of the get-naked-and-worship-the-trees course.