Hi. DM of the OP here.
I have to pretty much agree with this last post.
I'm not sure how I feel about alignment as being hard coded here (I don't think it caused the issue) nor did I think they really anticipated anyone to attempt to reverse engineer that which forced alignment change or what the repercussions of a forced change is.
Needless to say the situation is messy and I went with the idea that by passing atonement is a bad thing and can lead to really bad results and it only gets worse the more evil something is.