What happens if a wife leaves Islam? I've searched the Internet and asked a few people I trust and the answer is always the same. If a wife apostatizes from Islam the marriage is not valid any longer, and the children go to the father.
If you think about it, it makes perfect sense. Muslim men are allowed to marry women 'of the book' (meaning Jews or Christians), only if they agree to keep a Muslim house and raise the children as Muslims. I would think that would be a difficult thing in itself. A Muslim man has to find a chaste Christian or Jewish woman that is religious enough to be chaste AND willing to raise her children as Muslims. BUT things change when a Muslim man marries a Muslim woman (revert or not). If she leave Islam, she may no longer be willing to raise the children as Muslim.
The problem is, that this ruling would never be carried out in the west. Even if the husband was willing to give up his wife, no western court would ever give the full custody of the children to the father. Sadly this would mean that the child would probably be pulled in many different directions and have a struggle to keep on the straight path of Islam. Inshallah things like this are rare, and when it does happen may Allah Subhannahu Wa Ta'ala make it easy for them.