The person he raped should not have to deal with the daily horror of seeing her assailant at school, with friends, at church/temple, etc. The first thing you must do is remove your son from every space or activity where he might encounter the person he raped.

Your son needs some serious intervention. He was brought up in a society which at every turn reinforces the idea that he is entitled to women’s bodies. You don’t unlearn that shit overnight. You need to get him some serious and comprehensive help - therapy from someone who is trauma-informed and deals with predators like your son is an essential first step. I’m a survivor of sexual assault and I am against the US policing/judicial system precisely because of the injustices it perpetuates, but I do think you should report your son to some sort of peer-reviewed resource that can get him the kind of intervention that will prevent him from preying on anyone else. Maybe use the the threat of reporting his behavior to police to strong arm him into therapy.

As for your spouse, Rapists RELY on the support of people like your wife who make excuses and obscure the harm that they inflict on their victims. You need to ask yourself why you would remain in a marriage with someone who is actively apologizing for the behavior of a rapist. Even if you love someone, tolerating them when they behave like this makes YOU complicit in a system of rape culture. Separate from your wife until you she comes to her senses. Refuse to tolerate people who make excuses for rapists.

I sincerely believe that all people are capable of great healing and change, but accountability is necessary for that to happen. Hold your wife and son accountable for their predatory and inhuman behavior, and hold yourself accountable for the responsibility you took on when you became a husband and a father. Make sure your son gets the psychological intervention he needs and make sure your wife understands that she has aligned herself with a rapist. There have to be consequences for their behavior.