Well, for one thing, Hale will not the be naive youth in the clergy that he was when he arrived...laden with books and his head in the clouds and everything the church said and did was the right thing. We know that when the court accuses everyone who comes forward with logical rebuttals as attacking the court and Hale responds with, "Is every question an attack on the court?" that he is thinking for himself. He has already begun to doubt the veracity of the girls and their testimonies because of Mary Warren's waffling. Hale does come to believe that John Proctor and his wife, Elizabeth, are good people who are the victim of some horrible lies and play acting. He begs Elizabeth to persuade John to confess so that he may save his life...Hale believes that God would want Proctor to live through this ordeal to remain a logical, trustworthy, honorable figurehead of the community.
So, after all is said and done, I imagine Hale is quite disillusioned with the whole thing. It is quite possible that he leaves the church altogether, but more likely, he will use his experiences here in Salem to be a more inquisitive counselor and advisor for the Lord. I'm sure he will not take anything at face value or blindly from a book as he did when we first meet him in this play. He will take each case and the individuals in the case as they come and listen carefully to what everyone has to say before passing judgement.