Sin is one of the critical themes of Christian teaching, and if we look towards Roman Catholic theology, we can observe the categorization of the seven deadly sins. I'd suggest that, thematically speaking, "Good Country People" hinges around the sin of pride. Mrs. Hopewell and Hulga are both prideful in ways that make one another miserable. Hopewell is prideful in her self-identification with respectability. At the same time, Hulga holds a pronounced sense of intellectual superiority over the people around her, on account of her education and atheistic worldview. Meanwhile, there is Manley Pointer, who is able to exploit this pride, appealing to Hopewell's sense of country respectability and Hulga's intellectual pretensions. In that respect, their pride ultimately renders them vulnerable to manipulation.

In addition to being a story about sin (particularly the sin of pride), this story can also be framed as one about an encounter with evil. In many respects, Hulga (sheltered as she is) seems somewhat naive about the depths to which human depravity can sink. This will change, however, when she encounters and is taken advantage of by Manley Pointer (who is actually a con artist). Pointer is a victimizer, and in this, he represents a force of active malice in the world.

Flannery O’Connor lived in and wrote about the south. Most of her stories have themes of religion, race, and class.  In “Good Country People,” religion comes to the forefront.  As the story progresses, three different views of religion wage a battle for which there is no clear winner: the sinful Christian, the hypocrite; and the atheist.

The sinful Christian

Mrs. Hopewell brandishes her religion to place herself as a judge of people as decent and respectable. She is a sinner herself despite her attempts to use her Christianity as a barrier. Mrs. Hopewell tells Manley:

I think there aren’t enough good country people in the world! I think that’s what’s wrong with it… You don’t see any more real honest people unless you go way out in the country.

 Of course, this judgment of Manley is incorrect since he is a liar. The name "Hopewell" (hope well) characterizes the mother. She fails to see the world as a mixture of good and evil.  This leads her to assume that the world is simpler than it is.  Her sin is thinking that she as a Christian can make judgments about everyone. 

Hypocrisy

Manly Pointer appears to be the “good country people” representative.  He just sells Bibles and goes around the country trying to get the good book in people’s homes and make some money for himself.  In the barn loft with Hulga, the reader meets the real Pointer. He is the ultimate deceiver.  When he pulls out his perverted accoutrements hidden in a cutaway Bible, even Hulga, the atheist, is appalled. 

O’Connor uses Pointer as an example of the hypocritical aspect of society that pretends to be a Christian, but actually scams and hurts people.  He tells Hulga at her most vulnerable point:

The boy’s mouth was set angrily. “I hope you don’t think that I believe in that crap! I may sell Bibles but I know which end is up and I wasn’t born yesterday and I know where I’m going.”

To exacerbate Hulga’s humiliation, he steals her glasses and her prosthetic leg. He adds them to his perverted collection. Knowing that Hulga had felt superior to him, as he leaves her in the barn loft, he tells her that she is not as smart as she thinks she is.

This is not the first time that Manly Pointer has hurt someone.  Now, he will continue on treating people like fools and luring them into his deception. He stands as the representation of the evil aspect of man.

Atheism

Joy-Hulga’s life began in pain with a gun accident literally blowing off the bottom half of her leg.  From that point, she separated herself from her family and the rest of society.  Using her time earning degrees, she holds a PhD in philosophy.  Until now, she has professed absolute atheism. To Hulga, there is no god and there is no afterlife; life ends at death.

In an address delivered before a Southern Writers Conference, O'Connor commented on the wooden leg:

We're presented with the fact that the Ph.D. is spiritually as well as physically crippled . . . and we perceive that there is a wooden part of her soul that corresponds to her wooden leg."

Since this is the case, it is not surprising that Pointer's comment that it is her leg which "makes her different" produces the total collapse of Hulga's plan. She really wants that Christian “moment of grace.”  Her philosophical approach has not allowed her to admit this, not even to herself. Atheism, in the end, is not a reality.