has john proctors affairs with abigail made his relationship with elizabeth stonger

I would say yes. Elizabeth leaves much of what John did to his conscience. I suppose she knew her husband and could see the guilt eating at him. Elizabeth does lie for John but the fact that John publicly comes clean on his own accord (about his infidelity) makes their bond even stronger. Elizabeth is steadfast about the truth. It pains her to lie, especially for a husband who has been unfaithful. Still she does it out of love. John confesses out of love for his wife and to appease his guilty conscience. By the end of the play their bond is stronger than ever. Even though Elizabeth is being sent away and John to his death, Elizabeth is finally proud of her husband. He may have lost everything but at least he still has his name,