It's called phobia indoctrination. It takes many forms and is pervasive in the JW cult. The following is just what I can come up with off the top of my head as the reason for this behavior:
- JWs seen attending services in a church building can be deemed as having disassociated themselves from the JW cult and would thus be subject to shunning. Even though you did not invite her to attend, this fact creates a negative view of churches in general because of the disastrous consequences of going to one. Furthermore the JW rumor mill is a scary thing and she may fear for her status if you and her children are seen going to the church.
- Churches are a center of "false religion" "christendom" (christendom is exclusively used in a negative connotation in the JW loaded language) and "babylon the great." JWs are told to "get out of her" lest they share in her sins and receive her coming tribulation (i.e. death at armageddon).
- While there's been less focus on it these days, your wife was likely raised in an era in which fear of demons was pushed extensively and many JWs see churches and symbols of christianity (i.e. the cross or virgin mary) as potential sources of demonic possession or torment.
- The JW literature often gives counsel not to even enter a church for the funeral of a parent or a family member. There was a thread about a recent article (tried to find it but couldn't after a cursory search) in which an account was given of a woman with an unbelieving spouse that was attending the funeral of one of his parents (I think) and the account explained how she demonstrated respect for her husband by waiting outside the church for him. Now this may sound like something that would tell you that taking your children to the church would be fine, but in reality this serves to demonstrate to a JW that merely entering a church building for any reason is something to be feared and will displease god. Your wife doesn't want her children to be murdered by her god at armageddon so she wants to keep them out of the church.
- Churches are often held up as examples of money-grubbing organizations that do nothing to benefit their members (ironic, huh?) and this is yet another reason that they will have a negative view of them.
I'm probably forgetting more than I'm putting down here. The point is that there's a TON of indoctrination going on regarding so much as entering a church building (I think even cleaning one if you work for a janitorial company has been discouraged) and your wife can't possibly be expected to be able to sort through it all. It just hits her as a big emotional red flag of fear and terror and sadness for her children and she can't handle it and shuts down. It's designed to do this so that you can't get past it. It's designed to be a wall too tall to climb so she won't put in the effort even if you try to work through it with her.
That said, it might be something you can get past, but be patient and go slow because it's going to be difficult for her.