John Proctor wanted to be a Puritan at heart. Many people who participate in organized religions find it easy to partake in the rituals of a given faith, but to act according to the demands of the soul is a much more difficult, but honest pursuit.
Proctor was a sinner, he confessed his great sin and discussed it at length with those who were influenced by his sin. But the impact of his sin most affected him. When he turned to Abilgail in a lecherous relationship, he stained his marriage bed from that point forward. Unfortunately, Puritans failed to focus as much on the grace, forgiveness, and mercy that are offered in the Bible that they preached as on the sin that they committed. His personal conflict felt like it had no resolution, there was no method for reparation without forgiveness.
The authorities were similarly unmoved.
When John finally accepts his fateful punishment for a crime he didn't commit, I think he feels justice was served for the previous sin of lechery he did commit.
Proctor is also conflicted about the church itself. On one occasion, while being questioned by Reverend Hale, Proctor confesses to the fact that seeing his money in the form of gold candlesticks in the church hurt his faith. He is not at all sure he believes in the Puritan way anymore, although he is still a Christian. Witnessing the fiasco that becomes the Salem trials only reinforces his doubts. He even yells "God is dead!" at one point, in part to surrender and in part to speak what he feels is the truth of the time.
There is a level of dualistic conflict in John Proctor on both political and personal levels. On some spheres, both feed off of one another. The conflict he feels on a personal level about his relationship with Abigail, first for having it and then for having to disclose it is one where concealment is pursued, but eventually relinquished for the sunlight of transparency. In the same way, Proctor's criticizing of the proceedings help to be the first rays of light in helping to expose the fraudulent nature of the proceedings and processes in Salem for determining guilt or innocence. In the same way that Proctor struggles and eventually must reclaim his own name for redemption at great sacrifice, the insinuation is that the people of Salem, or any government, must do to the same to ensure that redemption and reclamation of one's political name can emerge as a possibility.
Proctor is in trouble with the authorities because he criticizes the court, making him appear as if he has been influenced by the devil. However, John’s internal conflict is really the major focus of the play. He is conflicted about sacrificing his reputation for the sake of truth. We see this when he struggles to make the decision to go to the court to tell the truth about Abigail, because he knows everyone will find out about his affair. He also struggles in his decision to sign a confession and ruin his name, even though, it would have saved his life.