In Act I, Elizabeth is not present, although she is mentioned by Abby. John is defensive of his wife as she is referenced as cold. Obviously he loves her enough to want to protect her.
In Act II, the act opens with John and Elizabeth having a cold interchange while she prepares food for him. He doesn't like the food and seasons it further when she is not looking. This might have been a symbolic gesture that he is making an effort to improve the situation. Their relationship stays stale through a conversation that essentially demonstrates she doesn't trust him anymore. He would like to make amends and improve their family. He is willing to "pay" for his sin by taking her wrath and cold shoulder, but he wonders when the treatment will end.
In the end of this Act, we find Elizabeth has been accused of witchcraft and John again comes to defend her verbally.
In Act III, after she's been taken and jailed, John confesses his sin in the court to demonstrate his moral character and a truth that only Elizabeth would know, but she lies to protect his name. They are obviously both trying to atone for their mistreatment of each other. She kept a cold house and probably drove him to find love in another, he was a lecher.
By Act IV, John is now in jail too. Elizabeth is pregnant, and the baby is John's. This symbol of new life may demonstrate that their relationship can begin anew, but the government has them bound away from each other. This new life foreshadows John's eventual inability to let Danforth make a liar out of John. John refuses to confess to witchcraft because it is not true. The telling of this truth earned him death, and Elizabeth watched in moral Godly pride that her husband did the right thing.