Part of what is difficult in regard to responding to the OP's question is we do not know what occurred when the couple married.
For example, let's say that this couple were married in the Roman Catholic Church. In order for this to happen (with the wife not being a Catholic), she would have had to commit to her children being raised Roman Catholic. (The RCC will not marry an inter-religious couple otherwise).
If she made a commitment to raise the children as Roman Catholic, it's no wonder that her husband would have an expectation that the children would be baptized as infants. Also, she would be in a bit of an ethical bind because she would have made a promise that she's not wanting to honor now.
Alternatively, if the couple married in a JP's office, or in another church, then it's a matter of negotiating these things with each other. It doesn't seem like it would be that difficult to come to some kind of compromise between the couple.