I agree with Cognac, find the new Scientology documentary to watch with her and it can cause some serious cognitive dissonence. Maybe not have an effect immediately, as she would likely bury the initial thoughts. But it should haunt her.The similarities are too great to ignore completely.
Make it a concern that you don't want your children exposed to Scientology so you want to make sure you both are well informed of their workings.Stress your disgust of Scientology specifically.
I do a lot of "seed planting" with my husband. Not mentioning the JW , but using other situations in other religions or government etc., to speak up about as he sits and agrees with me, sometimes speaking up with his own disgust or anger, until his face goes into this strange blank look, as he is processing the similarities. We don't talk about it, I just let it simmer within him. Maybe someday....
Watching the documentary about North Korea was another one. Sometimes I throw in a JW buzzword when describing something controlling/disgusting/just-plain-wrong ;-) Usually at the end of the discussion and I find a reason that I must do something else. But I keep an eye on his face for a while. It is interesting sometimes to watch the battle within his mind.