I suggest that your relationship with your boyfriend is the cause of this. Couples should not fight in front of their children. The fact that the two of you continue to fight indicates that you and he do not have a good relationship. Fighting is damaging to the children's emotional well being. Your son's reaction is justifiable. I'm glad that you want to put him first.
Yes, you are a part of the problem with the relationship. You, yelled and screamed too. That is one reason I suggest that the two adults need to be in counseling. Do no involve your son at this point. He is NOT a part of the problem. The problem is your relationship with your boyfriend and his immaturity in relating with your son.
I suggest that you and your boyfriend split until you can get your relationship back on track or find that it's not a workable relationship. Get couples counseling to learn how to resolve your differences without a fight. And.....when you do see a fight coming; it happens to all of us; learn ways to take it out of the awareness of your son.
Tell your son that you understand and even appreciate his efforts to protect you. Then tell him he should not have to be in that position and that you're going to work on your relationship with your SO by living separately for awhile.
I suggest it's imperative that you provide a break between your SO and your son. Your SO is acting in an immature way and your son should not have to be involved with him while he's holding a grudge. Make your son's happiness your primary focus.
What your son did is reasonable. I am proud of him. It would've been much better if he'd not been involved but since you involved him his reaction is normal. Do not try to teach him a different way of reacting. Accept what happened as the responsibility of the adults and do not blame your son.
Later: I just discovered that you have also asked the question about paranoid personality disorder. I know, based on professional education and experience that if you choose to stay with this man, you will be sacrificing your son. Whatever is causing your boyfriend to act this way, it is a serious illness and will require you to spend most of your time dealing with him, his immaturity and his paranoia. You cannot change your boyfriend. He cannot change himself. He needs massive psychiatric help which is expensive and time consuming. You will not be able to provide a safe and secure place for your son because you will never know what is going to happen next with your boyfriend.
I understand loving him. I understand wanting to stand beside him. You first made a son with a loving father. You owe it to your son and his father to first take care of your son. Your boyfriend is unable to love your son. He's shown that he is unable to even accept your son as a child. He expects more from your son than he expects from himself, behavior wise.
Please put your son first. He needs a safe and secure and full of love home in which to mature and become an adult. He needs to first be a child who does not have to protect his mother. He needs to not have to worry about you and your safety. He needs to know that your boyfriend, whoever it will be, will be loving and kind to both of you.
You have been asking your son to make allowances for your boyfriend. That is so very unfair to both you and your son. You are not responsible for your boyfriend and his mental health. You are responsible for your son and his mental health. You are responsible for providing positive experiences for him so that he will grow up to be a caring and responsible adult.
It's one thing to stay with the father of a child when he's an inadequate and abusive father. It's an entirely different thing to stay with a boyfriend when he's an inadequate and abusive father. A father and son will always have a relationship even if it's an unhealthy one. Your son does not benefit from a relationship with a man who is paranoid and immature. It may be worth working on a relationship with a son's father. There is nothing to be gained from working on a relationship with a boyfriend. Your son doesn't need a relationship with your boyfriend like he would with his father. Protect your son, now!