Praise be to Allah, the Lord of the Worlds; and may His blessings and peace be upon our Prophet Muhammad and upon all his Family and Companions.
There is no harm for a Muslim to marry a woman of the people of the book provided she is chaste, as Allah permitted this. Breaking off marital relationships could happen even if both the husband and the wife are Muslims.
As regards the fostering of the child (or children) when the husband divorces his wife of the people of the book, it is for the father according to the correct opinion of the scholars. Because the child is a Muslim like his father and she has no right or power on him (child).
It is feared in the case when the child stays with her that she brings him up according to non Muslim beliefs. If the country in which you live gives the right of custody of the child to the mother, and you cannot take him from her, so in this case, dear brother, you have to try your best to arrange meetings with him through which you can teach him the true creed i.e. the belief in Allah, and in His Prophet (Sallallahu Alaihi wa Sallam), and make him attracted to you by giving him what he loves, like clothes and money and so on. And when he grows up, he will InshaAllah choose the belief and guidance.
You have to know that what had happened is predestined. So you have to be patient and hope for the reward from Allah, and be optimistic for good things. Allah says: "And certainly, We shall test you with something of fear, hunger, loss of wealth, lives and fruits, but give glad tidings to As-Sâbirin (the patient ones, etc.). Who, when afflicted with calamity, say: "Truly! To Allah we belong and truly, to Him we shall return." (Al-Baqarah 2:155-156)
Allah knows best.