Students wept in the Department of Catholic Studies at the University of St. Thomas when the Rev. Michael Keating took a leave of absence last fall over a child sexual abuse lawsuit filed against him in St. Paul.

Few could reconcile the allegations in the suit — that Keating had abused a 13-year-old girl while studying to be a priest — with the charismatic 57-year-old professor known for his spellbinding lectures and aggressive defense of traditional Catholic values.

When the suit was filed, former Archbishop Harry Flynn and his top aide, who had known about the allegations, abruptly resigned from the St. Thomas board of trustees. The university launched its own investigation of Keating, including why university officials were not told about the alleged abuse, about a church investigation that raised some questions about Keating’s behavior with other women, or a set of recommendations that Keating’s contact with adolescents and young women be restricted.

“That was certainly not on my radar,” said Marisa Kelly, a former dean at St. Thomas who had responsibility over Catholic Studies from 2006 to 2011, a period when Keating was building his reputation in the department even as he was being investigated.

Keating has denied any wrongdoing. He declined to be interviewed for this story because of the ongoing lawsuit, but his attorney has said the allegations are highly defamatory and “thoroughly discredited.” Keating remains on indefinite leave from St. Thomas, and the university said Friday it can’t comment on questions related to the investigation.

Documents in the Keating case, like other recent disclosures about how the Archdiocese of St. Paul and Minneapolis handled clergy sexual abuse allegations over the past four decades, raise questions about the church’s willingness to disclose alleged or confirmed cases of abusive priests.

Since 2008, the archdiocese fought against releasing a list of priests credibly accused of child sex abuse, before agreeing to do so late last year. It continues to fight a court order to release a more sweeping list of any priest accused of abuse after 2004 because it says potentially innocent priests would be harmed.

Latecomer to priesthood

Keating did not become a priest until he was 46, but he has long been deeply involved in religion. In 1984, the Cleveland native joined Servants of the Word, a lay order of Catholic and Protestant “brothers” in Michigan who took vows of celibacy and dedicated themselves to “helping young ­people live faithful lives.”

Stuart Ferguson, a steward of the group near Ann Arbor, said Keating quit the order in 1995 but was in good standing. By 1997, he was a seminarian in St. Paul and in May 2002, he was ordained.

From 1997 to 2000, a police report said, Keating allegedly fondled the daughter of family friends, often while he read to her on the family couch. She was 13 and Keating was 41 when it began, according to the report. E-mails he sent her from Rome in 1999 and 2000 expressed love and affection.

The alleged victim, now 28, told family members about Keating’s behavior after she entered college. In 2006, she took her case to the archdiocese and to the Chisago County Sheriff’s Office. No criminal charges resulted and a clergy sexual abuse review board for the church concluded in 2007 that there was insufficient evidence to support a finding of child sexual abuse.

The evidence is described in memos written by the Rev. Kevin McDonough, then the vicar general and the archdiocese’s primary investigator of sex abuse claims. He used the phrase “inattentive seductiveness” to explain Keating’s relationships with several women before he became a priest.

A priest at St. Thomas who was a religious supervisor to Keating told McDonough and police that Keating told him he had a “passionate physical encounter” with an Italian teenage girl while in Rome. Keating told McDonough that his words “did not mean what they might appear to mean.” McDonough confirmed that the Italian girl flew to Minnesota for Keating’s 2002 ordination.

The memos also include a nun’s report that Keating behaved in a way that came across as “special” or “romantic” to four or five women before he joined the seminary in St. Paul. The nun said a woman in her 20s from Costa Rica was emotionally “bruised” by Keating in a relationship that had become romantic.

While the review board did not find child abuse, its ­opinion, released to the alleged victim in late November 2007, included a set of recommendations that Keating be supervised and limited in his contact with youth.

“The priest is to be restricted in activities in the nature of retreats, spiritual counseling, or mentoring, particularly of adolescents or young adults,” the review board ­recommended.

The board also recommended that Keating receive coaching, that his supervisors be notified of its findings and that a follow-up report be made to ensure Keating’s compliance.

Tamara Kaiser, a St. Thomas professor emerita of social work and an expert in supervisory relationships with a focus on boundary violations, said the recommended restrictions on Keating indicated strong concerns about his behavior.

“One would expect such recommendations to be forwarded to Archbishop Flynn and to the university and be implemented,” she said. “If that didn’t happen, something seems to have gone terribly wrong.”

Neither the university nor the archdiocese would comment on what happened to the recommendations.

Four months after the recommendations were shared with the woman who brought the complaint, McDonough circulated a memo to Flynn and two other archdiocesan officials. He suggested it was time to wrap up the investigation with a document that “should clearly exculpate Father Keating.” The memo did not mention any restrictions on the priest.

By then Keating was deeply involved in students’ lives, even beyond the classroom.

A star in Catholic Studies

With 250 students, St. Thomas’ Center for Catholic Studies is one of the largest and best known in the country. A celebration late last year to mark its 20th anniversary drew 600 guests, including Cardinal Timothy Dolan, archbishop of New York.

“When it comes to Catholic Studies programs, you are the New York Yankees,” Dolan said.

Keating is director of the Habiger Institute for Catholic Leadership at St. Thomas and an associate professor of Catholic studies. He joined the university’s full-time faculty in 2005 and won tenure and a promotion in 2011.

First as an adjunct professor and then as a full-time faculty member, Keating taught Catholic doctrine in various classes that students begged to get into. He headed St. Thomas’ signature Rome program, which sends upward of 30 St. Thomas students each semester to study at Angelicum ­University.

“Even in terms of cooking pasta, students took what he said as bible,” said Isaac Huss, a St. Thomas graduate who studied in the university’s junior seminary from 2004 to 2008.

In the May 2007 issue of the Catholic Studies magazine “Perspectives,” Keating wrote that “one important task of a Catholic university is to contribute to the honing of a ­genuinely Catholic mind.”

He also defended the Catholic Church as a “good and necessary” institution, writing in a paper featured last summer at a St. Thomas faculty seminar that Christ left behind an organization that became the “true home of the human race.”

Like other professors, Keating privately advised and mentored students. He also spearheaded the formation of men’s and women’s “Catholic Houses,” living quarters for groups of devoted students, according to meeting minutes from the Catholic Studies Advisory Board. Keating oversaw the application process and visited for weekly dinners at the first Catholic House for women when it opened in the fall of 2007.

Keating also led students in spiritual retreats away from campus and helped choose “Leadership Interns” for a program in which he and other chaperones led juniors and seniors on “Catholic leadership” excursions to France, Peru and Colorado, according to university publications and Advisory Board records.

“He was deeply involved in Catholic Studies and he genuinely loved what he was doing,” said Paul Wojda, a St. Thomas theologian and ethicist. “He loved to form young minds.”

He did it so well that Don Briel, the director of Catholic studies, believed Keating should be featured prominently in any marketing of the center.

“In any new strategy the department should highlight Father Keating and me since we seemed to have had the highest impact on student recruitment,” Briel wrote in a 2008 job performance self-assessment.

Outside the university, Keating was highly regarded by St. Paul church leaders and was recently chosen to be a speaker in the archdiocese’s important “Rediscover Catholicism” campaign.

Even so, a St. Thomas employee with knowledge of Keating’s tenure application said Kelly, the former dean, recommended against tenure because she believed his scholarship was lacking. Supervisors and colleagues of the priest in Catholic Studies rebutted the criticism, and Keating was granted tenure in the spring of 2011.

Kelly, who became provost at New York’s Ithaca College in the summer of 2011, declined to comment.

Doug Hennes, a spokesman for St. Thomas, said the school’s board of trustees has established a committee to review findings of the investigation, expected by the end of May. The university will decide at the conclusion what information to share with the public, he said.

The woman suing the priest said in an interview that the archdiocese’s decision to keep Keating in active ministry “re-victimized” her.

“I think they did believe me,” she said, “but Keating was more important to them.”