Your husband needs to stop blaming you and stop treating your son like he is defective and start owning his feelings about his own circumcision. I understand how hard it can be for men to face their insecurities and I sympathize, but still, it's time to grow up already. Be a man. Own your feelings, deal with your problems, stop blaming your wife and innocent son. Get professional help if necessary.
As for your question of whether you are doing the right thing, well, if your husband was angry and upset at you and the only way to make him feel better was to cut off your daughter's earlobe, would you even pause a split second to decide what was the right thing to do???? And earlobes really are pretty useless, aren't they. You stated that if you circ'd your son, you would be doing it only for your husband. Sorry, but we just can't go around doing cosmetic surgery on one person to make another person feel good. You ARE doing the right thing. Perhaps one day your son and maybe even your husband will thank you for standing up and doing the right thing.
I'm sorry he is putting you through this difficulty at such a vulnerable time in your life when you most need support. I hope that things get better for you and for him.
You asked how it might affect the father-son relationship in the future. That, too, is completely up to your husband. If he is going to treat your son like a freak, if he is going to go around with a cloud of resentment because your son did not have cosmetic surgery, then it sure won't be good for their relationship. And there's only one person who can do anything about that.
I'm sorry if I sound callous towards your husband. I don't mean to. I feel for him, I really do. I know a number of circumcised fathers of intact boys, my husband included, and I can only imagine how difficult it is for them. He is probably in a place now where he is hurting so bad that he can't even admit to himself that he is hurting. That is so sad. That is how circumcision harms. Even now, 20, 30, 40 years after the fact (I don't know how old your husband is), his circumcision is still causing problems for him. It's interfering with bonding with his son, feeling good about himself, and loving and supporting his wife. How sad is that? But, the main thing is, he has to realize that it is his problem and that it is unfair (to say the least) for him to expect his infant son to give up a body part (forever, and at great pain and risk to his health) just so Dad can go on pretending he doesn't have any issues.
Best of luck to you, and here's to healing and happiness for your husband!