All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad is His slave and Messenger.
The scholars differed in opinion about the wife if the father of the husband had committed Zina (adultery) with her whether or not she becomes forbidden for her husband. Some of them are of the view that she becomes forbidden for him, and others are of the opinion that she does not become forbidden for him, and this is the most preponderant opinion because in principle what is forbidden does not render forbidden what is lawful. Therefore, this woman does not become forbidden for you just because she was raped by your father and this does not prevent you from continuing the bond of marriage with her.
As regards her statement that she cannot live with you, if she means that she has become forbidden for you, then her statement is not correct.
With regard to the child, he is traced back to you because he was born on your bed (i.e. during your legitimate marriage), and it is confirmed that the Prophet said: “The child is for the owner of the bed.”
There is no doubt that what your father did with her is an abominable act and you should be careful for this matter not to happen again. So, it is not permissible for your wife to allow him to be in seclusion with her as he is suspicious, and she should treat him like a non-Mahram.
For more benefit, please refer to Fataawa 121303 and 92408.
Allaah Knows best.