Sounds to me like the husband's eyes need to be opened as well. If he's an atheist, and threatening to take the kid and go if she goes to church, he is clearly not committed to the marriage. The nephew must be aware of this at some level. If he's not committed to the marriage, then he's not committed to the family. I would question whether a valid (in the eyes of God) marriage exists, as when he said "I do", he probably didn't mean the same thing as a Christian means when saying "I do." A Christian intends to start a family and all of the committments that entails, and he's not committed to a family.
A father is extremely important to a child. A lack of committment to the family, even if he comes home and eats dinner every night, will certainly hurt that child, and lead to behavior problems. It may be necessary for another mature male family member to take on some of that role (hint, hint

) It is very important that the family establishes a good relationship with God. If he wants to go, I'd say let him.
I have a cousin who was in a similar situation. When she started going back to church, the atheist husband was extremely resentful. He became abusive to her, distant from the children. Eventually she had no choice but to leave him, or have him teach their children how to abuse women. I'm not normally in favor of a divorce, but if there's no committment to a family and what that entails at the time of the wedding or anytime thereafter, it can be argued that a real marriage didn't exist in the first place despite the verbal exchange of vows. In that case, if he wants to go, or if he's hurting the spouse, by all means it's okay if he's out of the picture.
just my 2 cents.
I'll pray for them.
happybrew