Confronting Abigail in court requires more than just Proctor telling what she told him earlier about the girls not really being afflicted by witchcraft ("She’s only gone silly, somehow. She’ll come out of it"). He knows that once he admits this to the court they will want to know how he came to know this. Why would a young girl confide this in an older, married man? He will have to admit that he had an affair with Abigail. While this seems small in today's media, this scandal would have rocked Salem. Adultery, or lechery, was a punishable crime that broke their laws (remember religion and government were closely tied).
His fears come true when he must finally admit that he “has known” Abigail. To the audience we realize that he is willing to tell the truth and tarnish his good name in order to do the right thing. Unfortunately, the court is still not willing to listen.