she treats me and our sons like shit, not affectionate (not that she really ever was...i blame on being brought up in a cult)
I think this part I relate to (although I am not in a heterosexual marriage with two children, please read on). This is how my mother used to behave. She had no problem being a total b to her children and husband.
Something that helped me was using her own nonsense against her. My father did the same thing. "I'm not a JW but I'm still the man of the house". If showing all the doctrine flaws that the WT has in their teaching and their actions doesn't work, maybe putting in practice an emphasizing all the crap that women in the JWs have to put up with just for being women may help her open her eyes. Every time that there's a disagreement remind her that JW or not, you are still a man, and the man of the house, and according to the JWs, she have to be submissive to you. You are the one running the house and she has to follow according to the JWs, and if I remember well, for as long as you don't interfere with her JW nonsense, she must obey you.
She cannot pick and choose which JW doctrine she will follow in the house. Some manipulative people do that --it, some people are JWs only for what is convenient to them.
She is hurting the family, her own children. Something should be done about it.