As with many of O'Connor's stories, there are several conflicts in this story, but two most important are 1) the conflict between what appears to be true and what is actually true and 2) the conflict between Joy/Hulga and Manley Pointer--the second is arguably the central conflict.
After Manley Pointer arrives at the Hopewell's house and has dinner and conversation with Mrs. Hopewell and Hulga, Mrs. Hopewell's judgment of Pointer is that "he was just good country people," a simple, harmless, sincere, Christian Bible salesman, "just the salt of the earth."
Although Hulga is suspicious and critical of him, as she thinks about him, she begins to see that she might be able to seduce him, an act in which Pointer would finally lose his simplistic Christian view of the world and, more important, his innocence would be gone, and Hulga could help him "with a deeper understanding of life." In other words, Hulga-as-teacher will take this innocent student and enlighten him and teach him that there is a wider world beyond his Bibles and simple outlook on life.
The conflict, of course, is that there is a meaningful difference between Pointer the simple Bible salesman and Pointer the sexual predator. When he finally shuffles off his cloak of innocence and reveals himself to be somewhat perverted, he manages to take from Hulga the item that defines her being, her artificial leg. With that leg goes Hulga's own type of "innocence," the belief that her intellect allows her to judge the world and its people accurately. Probably for the first time in her life, her intellect has failed her completely. We don't know, of course, what this incident actually did to Hulga, but we can assume her self-knowledge and self-absorption changed dramatically.
The good country person has managed, because he looked and talked the part, to fool Mrs. Hopewell and Joy/Hulga, but Mrs. Freeman, the tenant farmer, has the last word (literally) on Manley Pointer when she says that "some can't be that simple."