I don't remember having Medea's master treason shown in the VN either. But it seems it allowed the scenarist to change her background enough that she's still a villain, but lovable one.
I'm pretty sure she didn't kill the girls, she might be a feminist too... I don't know why I feel that she might be though.

Changing our view on Caster allows to change the Villains chart a little, now Caster isn't as bad as Kotomine... she's in the Villains bracket too, but could have been saved at any time, while Kotomine is a plain bastard with nothing to save.