Mr. Thornton's innate decency of character is displayed in a couple of ways in these chapters. First there is his quiet attendance at the funeral where, unnoticed, he pays his respects to Mrs. Hale. Despite his anger and belief that Margaret has a secret lover, he stops Dixon and enquires how Mr. Hale and Margaret are doing. Dixon's reply that Margaret is holding up well is perhaps a little unfortunate, because it leads Thornton to assume that she is drawing strength from her relationship with the man he saw her with at the station. He is of course wrong, and so is Dixon; Margaret is not actually doing that well as we soon see.
Perhaps the best indication of Mr. Thornton's character is when, soon after the funeral, he pays a condolance call to the Hales. When Margaret is called out of the room to speak to the inspector, Mr. Hale is able to open up to Thornton about his grief and loss as he has been unable to do to his daughter. Thornton, who with Margaret has been unable to express his feelings easily or eloquently, finds words of comfort and faith to strengthen his sorrowing friend: "They never spoke of these things again, as it happened; but this one conversation made them a peculiar people to each other; knit together, in a way which no loose indiscriminate talking about sacred things can ever accomplish."
Though there are no legal repercussions for her lie due to Thornton's intervention, the situation has a lasting impact on Margaret. Throughout her time in Milton, Margaret's character has been gradually undergoing change and refinement. This crisis completes that transformation: she loses any sense of moral superiority. Knowing herself to be in the wrong- though to protect her brother- she is humbled, ashamed, and repentant. She now considers Mr. Thornton to be her superior and this brings her to a startling realization: she cares about what he thinks of her, and it hurts to know that he must now despise her.