Hm, I tend to agree with morriswalters, Mr. Death, and Mira. Bad Alias makes some very good points as well. I think my ideas of Margaret are a tad different. I think that while she ultimately had a good heart, but she was running with a bad crowd for a reason and I think part of her liked the power that came with it, if only so she could use it to do good.
Narrative wise, I bet she's a dark reflection of Harry and when he finds out, it'll really throw him for a loop before he ends up believing that she did end up redeeming herself. I have a feeling that she might actually had a harder time dealing with her darker side than Harry had. Plus, I think this would be fairly interesting.
I also think that a lot of her calculations for how Harry came to be were both intelligent but also desperate. I think she overestimated her intelligence and it came back to gite her in a really big way. Maybe her creation of Harry was more of a last ditch attempt to combat outsiders. I don't know if Thomas was an accident or not; she did leave him, despite not wanting to.
I know that people were comparing Morgan and Margaret's situation to Lily and Snape, but what if in this variation, Margaret is Snape?