Praise be to Allah.
It is permissible for a Muslim man to marry a Christian woman, if she is chaste. Because Allaah says (interpretation of the meaning):
“Made lawful to you this day are At‑Tayyibaat [all kinds of Halaal (lawful) foods, which Allaah has made lawful (meat of slaughtered eatable animals, milk products, fats, vegetables and fruits)]. The food (slaughtered cattle, eatable animals) of the people of the Scripture (Jews and Christians) is lawful to you and yours is lawful to them. (Lawful to you in marriage) are chaste women from the believers and chaste women from those who were given the Scripture (Jews and Christians) before your time when you have given their due Mahr (bridal-money given by the husband to his wife at the time of marriage), desiring chastity (i.e. taking them in legal wedlock) not committing illegal sexual intercourse, nor taking them as girlfriends”
However it is not advisable to marry a kitaabi (i.e., Jewish or Christian) woman nowadays, because it is fraught with dangers, especially with regard to the children’s upbringing.
Shaykh Ibn Baaz (may Allaah have mercy on him) said: If the kitaabi woman is known to be chaste and to keep away from the things that lead to immoral actions, then it is permissible, because Allaah has permitted us to marry their women and eat their food.
But nowadays there is the fear of great evil for those who marry them, because they may call him to their religion and that may lead to his children becoming Christian, so the danger is great. In order to be on the safe side, the believer should not marry her. Moreover, there is no guarantee that she will not fall into immoral ways, and attribute to him children who are not his. But if he needs to do that then there is nothing wrong with it, so that he can keep himself chaste and lower his gaze, and he should strive to call her to Islam, and beware of her evil lest she drag him or the children into kufr (disbelief). End quote from Fataawa Islamiyyah (3/172).
Hence you can see that the Christianization of the children is one of the greatest dangers to be feared as a result of marrying a Christian woman. Undoubtedly it is not permissible for you to allow that under any circumstances. You should have made it clear to her before marriage that your children would be Muslims and that they could not be made Christians, and that this issue was not open to discussion or compromise.
What you have to do now is protect your son’s religion and prevent him from being made a Christian. If your wife insists on that then you have no choice but to make her stay with you in your city, or keep the child only, even if that leads to you leaving her and divorcing her. This is a serious matter, because it is the matter of kufr and faith; we seek refuge with Allaah from misguidance.
It should be noted that the child’s being baptized does not actually make him a Christian, rather he is a Muslim who follows the religion of his Muslim father, and he cannot become a Christian unless he understands Christianity and chooses it for himself. As for his baptism, he has no choice in the matter, and it does not affect the religion which Allaah created in him, which is Islam.
Try by all means to protect this child and prevent him being taught Christian teachings. Remember that you are responsible for him and that the worst neglect and betrayal of this trust would be to leave him disbelieving in Allaah.
We ask Allaah to protect you and your offspring and to divert evil away from them.
And Allaah knows best.