BUENOS AIRES, Argentina -- The elevation Wednesday of Argentine Cardinal Jorge Bergoglio as the Roman Catholic Church’s 266th pope and the first from Latin America brought cheers across South America but also served as a reminder of the church’s role during the region’s dark days of dictatorship in the latter half of the 20th century.

Born in Buenos Aires in 1936, Bergoglio, 76, was 40 when Argentina’s military overthrew the government of Isabel Peron and instigated what became known as the “Dirty War,” during which as many as 30,000 people, most of them accused of being leftists, “disappeared.” Like many priests his age, he has been accused of not doing enough to protest the carnage.

In 2005, Argentine author Horacio Verbitzsky, whose books have detailed what he said was the church’s involvement in the Dirty War, accused Bergoglio of failing to protect two fellow Jesuits who’d opposed the military junta. The two Jesuits vanished and were presumed to have been killed by security forces. Bergoglio was never charged in subsequent years, nor has any hard evidence emerged of his involvement. But the charge has lingered largely because of Verbitzsky’s prominence in Argentina.

More recently, Bergoglio has been known for his confrontations with Argentina’s last two presidents, the husband and wife team of Nestor and Cristina Kirchner.

"He was always very kind to the poor and the drug addicts, I hope he can keep those qualities in the Vatican," said Roberto D’Abbraccio Varela, 63, a Buenos Aires security guard and Roman Catholic. “There are some doubts with him about what he did during the military dictatorship but you can never know the truth and since he was never judged we have to presume he’s innocent."

Nestor Kirchner, who died in 2010, famously accused then-Cardinal Bergoglio of being “the true leader of the opposition.” During Argentina’s financial meltdown in 2001 and 2002, Bergoglio was a constant voice for the poor. He later famously lamented the rising poverty in Buenos Aires, noting that residents there “take better care of a dog than a brother.”

Bergoglio also was cool to Kirchner’s efforts to annul amnesty laws that protected those accused of crimes during the Dirty War. Among the first people to be tried after the laws were abolished was a Catholic police chaplain. Christian von Wernich was convicted and sentenced in 2007 by a federal court for participating in a series of crimes it said were “akin to genocide.” At the time of the trial, Bergoglio headed Argentina’s Conference of Bishops.

A common theme during the trial was the church’s inaction. One witness during the trial, the Rev. Ruben Capitanio, told the courtroom, “I say this with pain. Until the church recognizes its errors, we will be an unfaithful church.”

He closed his testimony by telling family members of the victims that “I apologize for still not being the church that we must be, on the side of the crucified and not the crucifiers.”

In a cable to Washington dated Oct. 11, 2007, Tony Wayne, then the U.S. ambassador to Argentina, noted the heavy political content of the case and the possible impact on Cardinal Bergoglio’s ability to oppose Kirchner’s policies.

“Many on the political left allege the church was complicit with atrocities committed by the state and believe the church has failed to account or atone for its actions,” the cable said. “The church has not yet disciplined nor defrocked Von Wernich but has sought to distance itself from the unauthorized, maverick operations of rogue priests. Nonetheless, at a time when some observers consider Roman Catholic primate Cardinal Bergoglio to be a leader of the opposition to the Kirchner administration . . . the Von Wernich case could also have the effect, some believe, of undermining the church’s (and, by extension, Cardinal Bergoglio’s) moral authority.”