(I am a terrible terrible fangirl and haven't seen any of S2 yet, btw.)

My headcanon is that Milady's actually been more truthful than most might expect when it comes to what happened with Thomas. That she truly loved (and still loves, but the hate is easier) Athos, and Thomas wanted her for himself. So he dug into her past, found out she was lying about everything, and threatened to tell Athos if she didn't sleep with him. When she still refused, he tried to rape her. But her killing him wasn't a heat of the moment act of self-defense; it was as cold and calculating as she is about most things (that don't involve Athos).