Maybe, but comes off pretty weak if you cut out the religious aspect of it. Much of her suffering was due to her believing that she was sinning, which was enforced by the nuns who are "god's representatives" on Earth. In a child's mind their authority is above question. "Using a sister without using a sister" might be passable for new readers, but for older fans it comes across as pretty lame, and messing with continuity.
Comes off pretty weak again as he wasn't the one who directly inflicted the pain. I can't see Aurora turning to the dark side to get even with someone not directly involved with the abuse.
They can't use Walter as he'd be getting the brainwashing treatment too. Plus, Aurora was the personality that wanted, and pursued the relationship with him, while the Jeanne-Marie personality, though disliking Walter, didn't hate him, and would be too moral to seek revenge, especially on someone who is helpless.
Sorry, I just don't see the sexual abuse version to be so awful that it can't be used. Besides, it would be far more likely to explain why her mind split along sexual lines; her Aurora personality being promiscuous while the Jeanne-Marie personality is prudish.