What is the irony in the story, including the names of the characters and the actions in "Good Country People"?

The irony in this story is mostly situational. This means that certain expectations are created, but the actions of the characters or the circumstances in which they find themselves are the opposite of these expectations.
The title and the story itself depict a stereotypical view of so-called good country people. The reference is to people who live in rural areas and lead simple, conservative lives. They are generally not well educated and have deep moral and religious values. They are hardworking and know their place. Their goodness derives from the fact that they are respectful of others and would, generally, not deliberately mean anyone any harm. They are guided by deeply entrenched codes of conduct mostly based on a religious ethic.
The story revolves around the relationships and interactions between Mrs. Hopewell, a divorcee, her thirty-two-year-old daughter, Joy, and their employees and tenants, Mrs. Freeman, her two daughters (the eighteen-year-old Glynese and the fifteen-year-old married and pregnant Carramae), as well as Mr. Freeman.
Most of the action revolves around Mrs. Hopewell, Joy and Mrs. Freeman. Mrs. Hopewell sees the Freemans as "good country people." She seems to have a cordial relationship with them and is quite close to Mrs. Freeman. It is clear that it is the Freemans' good nature that compels Mrs. Hopewell to hire them and provide them tenancy on her farm. They have been living there for four years.
Joy suffered a terrible injury when she was twelve and lost half her leg. She has a stump and is well educated, having obtained a PhD in Philosophy. She is an atheist and comes across as quite cranky and sometimes expresses frustration at her situation. She has never shown an interest in the opposite sex--a factor which doesn't seem to bother her mother too much.
Most of the action in the second part of the story revolves around the interaction between Mrs. Freeman, Joy, and a young Bible salesman who calls himself Manly Pointer. Mrs. Freeman is quite impressed with the young man's honesty and invites him to stay for dinner, although she refuses to buy one of his bibles. 
The end of the story exposes situational irony on different levels: Firstly, Joy behaves completely out of character and, to her mother's surprise, seems to enjoy the young man's company when she accompanies him to the gate.

Then to her amazement, Mrs. Hopewell saw the two of them walk off together, toward the gate.

Secondly, Joy plans to seduce the young man and later thinks that her seduction has been easy, but it later seems as if he has actually seduced her and only allowed her to believe otherwise.
In the third place, it is ironic that Joy decides to be honest and confess her age whilst Manly has been deliberately misleading all along. He later tells her that he's not religious at all:

"I hope you don't think," he said in a lofty indignant tone, "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!"

He also informs her that he had lied about his name. It is clear that he had planned everything carefully since he seems to have a sick obsession with collecting objects related to disability, such as her wooden stump. His idea, from the outset, seems to have been to draw her into a lewd sexual encounter and then take her stump. He declares:

"I've gotten a lot of interesting things," he said. "One time I got a woman's glass eye this way. And you needn't to think you'll catch me because Pointer ain't really my name. I use a different name at every house I call at and don't stay nowhere long..."

Irony is also found in the fact that in spite of her PhD, Joy has easily been fooled by someone much less educated than her. Manly tells her, "you ain't so smart." Furthermore, it is also ironic that she has been misled by her belief that he is "good country people" when he, in the most disgusting sense, obviously is not. Joy expresses her shock at this realization when she asks:

"Aren't you," she murmured, "aren't you just good country people?"

To which he replied:

"Yeah," he said, curling his lip slightly, "but it ain't held me back none. I'm as good as you any day in the week."