Violence against an innocent girl
Rape itself is highly ironic, because it involves an attacker using the mechanisms for love and unity (sex does accomplish those things in the right context) for evil purposes. The issue of innocence is ironic, because Marianne loses her innocence without becoming guilty of anything. She is innocent, even if she made mistakes. Oates underscores this by showing Marianne's full-blown alcoholism.
The identity of the assailant
When Marianne's father learns the identity of Marianne's rapist, he realizes that he knows the boy's father. They've done business together in fact. Suddenly, he is perplexed, knowing he has shaken hands with the man who raised a boy so evil that he raped Michael's only daughter. The irony is deepened by the fact that a boy would commit such evil against his own schoolmate.
Privacy and justice
When Marianne decides to keep the rape a private matter, her father ejects her from their home. That's how unfathomable the events seem to Mr. Mulvaney. But it's also an indication of a deep, private turmoil that rape victims know all too well: If they seek justice, it will come at the expense of their privacy and reputation. Her father's strong opinions are another kind of misogyny against Marianne. He throws gasoline onto the fire by refusing Marianne the privacy and autonomy she deserves. In other words, he treated her with misogyny when she was already the victim of misogyny.
The murder
The complicated situation becomes even more complicated when one of Marianne's brothers takes justice into his own hands and murders the rapist. It's easy to cheer at the death of a known rapist, but the reader should remember that the brother's decision to make things about himself instead of honoring the will of his sister is misogyny in that he takes the issue out of Marianne's control. Also, death is a complicated fate for anyone, and to take another life might have unjust implications of its own. Although the murder seems fair, it's another act of violence.
The denouement
A denouement is the part of a story that comes after the plot resolves, during which the reader gets a sense for what might have happened to the characters. Oates does something unusual (especially given her propensity for dark, difficult themes). She gives the family a chance to reunite. Fifteen years from the incident, the family finally finds peace and harmony. This beautiful irony is the gift of hope.