"Long story short the JWs have created a void in our relationship and I have filed for divorce for a couple reasons, but I'm worried about the JW upbringing being inflected on my daughter. "
Since you are going to have some type of joint custody you should come out of this in decent shape. And have the privilege of helping your daughter to think for herself.
However what is a more serious influence are the personal friendships she may make in the Kingdom Hall with kids of her age who come from serious JW homes.
The counter to this is to encourage her to make friends at school and also get involved in after school monitored events. If she has a foot in both worlds she will have an opportunity to think for herself.
The JW's are terrible with children it's just not their nasty pedophile problem but their call for a life time of obedience to whatever they can dream up.
It doesn't sound like her mother is going to function on her own......nor stay committed to the strict beliefs of the JW's.
If the subject of getting baptized comes up do mention that Jesus was thirty years old when Baptized.
There is a bunch of stuff we can discuss based on so many of us who had to deal with and survive the JW world.
P.S. You need to talk about the JW ban on blood transfusions in your custody agreement and need to be immediately notified if she needs a life saving transfusion.