Why not buy the books for your D11 and keep them at your house. Clearly your W does not feel the same way about prayer/raising children at this time and it does feel like you are pushing beliefs IMO.
I wouldn't per say ask your W for permission to have your D11 read these books but perhaps say something like: W, I bought D11 some books that I am going to keep at my house for her to read. Why don't you work on the American Girl books w/her and I will work on the books we have here. Who knows, with some consistent reading at both our homes maybe it will become less of a chore for D11 to read and she might actually learn to enjoy it.
Reading is a great thing. Why don't you implement some sort of reading hour with your girls a few nights a week. Go buy some big comfy floor pillows and find a little corner of your apartment that can be reserved for the "reading area". Let your kids be part of creating the reading area. Get them excited about it!
As far as your W thinking/justifying that the separation is not part of D11's behavior issues it might not be the root issue as you said she had anger issues prior but it certainly plays a part now. Your W might never acknowledge that and trying to point it out to her is fruitless.