Is your son involved in anything Step Dad can enjoy with him? Little league, soccer, cub scouts? If not, have him join something, anything. Then have dad take him. Have dad be the good guy. This will be hard for dad because he wants to be the discipinarian, but you have to be the one to put your foot down. You have to be the one to say it's like this.
If you allow this to fester it will tear them apart and you will have huge physical fights on your hand.
Sit hubby down and tell him you need him to be the hero for your son. Your son needs him. HUbby needs to put his hurt feelings aside, because he is hurting, you took juniors side or junior took yours, and he needs to be the man who has all the answers. He needs to be the man that is fun to be around.
Does hubby have a workshop? Does he fish? Do you all camp? These are good man/son activities.
I have lived this feud for 15 years. The only reason my son and husband are now on speaking terms is because the boy is in the Navy doing exactly what my husband does in the Marines. Go figure.
One thing, hubby's dont' like wives to tell them what to do. So go to a counselor and have the counselor tell you what you would tell him anyway. That way its' the doctor said......
Good luck.