Not quite the same, but similar enough, I hope.
I live in a community where Christian parents must basically brainwash their children or else face social suicide. Though the church power isn't very... 'powerful' here, what areas of life it does dominate it holds with an iron grip. I remember when I told my first big lie. I claimed I was Christian in school to avoid the bullying. This is relevant because the bullies, and myself, were only SIX.
These same kids, I knew all throughout elementary, middle and high school, and let me tell you, you probably have the right to be disgusted. These bible kids either grew up to be ignorant sheep or incredibly rebellious druggies. If you care for your ladyfriend's kid at all, and you trust my experience growing up and watching these kids for years, immediately take action and take the kid out of that group.
As for the selective teaching, I think that's just a human fault...
I don't yet have kids, but I imagine that a part of their well-rounded education will include world religion. Regardless of the belief aspect, religion drives the behavior of others around them, and they will need tools to approach this behavior. I don't, however, imagine this eduction will involve shipping them off to a class on christianity once a week at the expense of lessons on other religions, topics, and critical thinking. That being said, it was in these classes at a later age, that both my boyfriend and I started to notice the sting of hypocrisy in some wide-sweeping statements that they made. Fortunately, despite their best efforts, our parents and teachers taught us to question, doubt, and explore, and that is a bud that may grow into skepticism. A more effective approach with your fiance may be to ease up on objecting to what she is doing, and instead suggest further educational activities and outings that promote critical thinking. There are several fun activities for kids of all ages to help them start to explore the world. Then you're not pushing your so-called "atheist beliefs," but rather promoting family bonding, learning, and growth. Just be careful not to overtly juxtapose these activities with your previous discussions regarding the kids group - if you do, be prepared for some massive counter-control and rationalizations.