He challenged a suggestion that the demonstrators were exercising their First Amendment rights.
"It was a terrible infringement on the rights of people trying to worship," O'Connor said. "It was very much a violation of our First Amendment rights to worship."
And, speaking in a taut, angry tone, he called the hurling of Communion wafers to the cathedral floor a "chilling, horrifying desecration."
"No demonstration," O'Connor said, "will bring about any change in church teaching. If the aim was to change church teaching, let me say the church will be teaching that abortion is the killing of human beings, (and) that homosexual activity is sinful, until the end of time."
New York Mayor Ed Koch, Mayor-elect David Dinkins, Gov. Mario Cuomo and several religious leaders also condemned the disruption, which forced O'Connor to abandon the homily he was to deliver.
"It was unacceptable," said Koch. "I hope the courts are taking this seriously."
"I deplore it," said Dinkins. "Peaceful demonstrations are one thing, but one should not disrupt a religious ceremony."
Andrew Humm, spokesman for the 50-group Coalition for Gay and Lesbian Rights, which has taken part in several gay rights protests at St. Patrick's, also condemned the demonstration inside the cathedral.
"If was horrifying," Humm said. "We endorsed the demonstration outside the cathedral, but the point was lost by what happened inside. We condemn the acts of people who disrupt worship services."
The protest was organized by the AIDS Coalition to Unleash Power (ACT-UP) and Women's Health Action and Mobilization (WHAM).