Hi,
Here’s how they work:
1. If I had a choice, I’d rather I never knew you. → Awkward. Better: “I’d rather I had never known you.”
2. If I had a choice, I’d rather we never met. → OK, casual and understandable.
3. If I could go back, I’d rather we never met. → Good and natural.
So #2 and #3 are fine. #1 needs revision.