I agree with the posts above in saying that there is no contradiction or real line between being broken/flawed and being honorable. In John Proctor's case, we see a man who has found his sense of honor in admitting to his flaws.
For sake of discussion, if we have to choose one side or the other I would say that Proctor is more broken/flawed over the course of the play. He is striving to fix what's broken about him. This is at the root of his character. (Though, this effort to fix what's broken and to admit to his flaws is also what makes him honorable.)
I agree. Broken and flawed are not adjectives exclusive to dishonorable people. Plenty of really good people have made really big mistakes; it's part of how we learn and grow. I think of King David in the Bible, who lusted after his neighbor's wife and had her husband sent to battle (where he was killed) so he could have her. Yet he repented and was called a "man after God's own heart." The key, of course, is understanding one's flaws and demonstrating a willingness to repair the wrongs and change one's ways. Proctor does that in the end, when he makes his peace with God and is able to both repent and forgive himself for his great sin. We don't see or hear those particular words, but it's obviously what happened or he would not have died at peace.
I would say that John Proctor is both flawed and honorable. Proctor had an affair with Abigail when she was a servant in his house. His wife has been unable to forgive him for this, and their marriage is unhappy until his wife, Elizabeth, is accused of being a witch by Abigail. Abigail even tells Proctor what really happened on the night the girls were discovered in the woods, but Proctor doesn't share this news with anyone until it's too late. Once Proctor is arrested for witchcraft, he's willing to admit to the charge, eveon though it's false, in order to save his life. These are all examples of Proctor's flawed character.
On the other hand, Proctor is known as a good man who is fair and is a hard worker. He is an honest man who regrets breaking his marriage vows. It is at the end of the play when Proctor is most honorable. Even though he has agreed to admit to witchcraft, he refuses to name any other people of his community. He also tears up the paper he has signed admiitting witchcraft when he learns the paper will be exposed for all to see because he says a man's good name is all he has to give to his children. To Proctor, his name is the essence of his character. If he allows Danforth and the other judges to take away his good name, then he also allows them to steal his soul. John dies an honorable man.