The sentence, the first for a Catholic leader for enabling clergy sex abuse, fell just short of the maximum seven-year term Philadelphia prosecutors had sought. It was hailed by victims and advocates who had complained that church officials long eluded justice for accommodating or concealing priests' attacks on children.
Lynn's lawyers had urged probation or a county jail term, and were disappointed at a sentence they said was disproportionate to the defendant and his crime, a single count of child endangerment.
The Archdiocese of Philadelphia, which paid for Lynn's defense but has been largely silent about his case, also questioned the sentence.
"We hope that when this punishment is objectively reviewed, it will be adjusted," it said in a statement.
Clad in his black clerical garb and white collar, Lynn told the judge that he was sorry for his "failings" during the 12 years he worked as Bevilacqua's secretary for clergy.
He spoke briefly and softly, repeating a mantra he first issued from the witness stand during his trial - that he did his best given limited power.
"But the fact is, my best was not good enough - and for that I'm truly sorry," he said.
Under state guidelines, Lynn will have to serve at least three years in prison before being eligible for parole.
Even then, his chances of getting out after serving the minimum could be slim. The state parole board has been reluctant to grant early release to inmates convicted of sex crimes involving children.
On June 22, a jury found Lynn guilty of endangering children by not removing a priest in the 1990s after discovering the cleric had once molested a teen. That priest, Edward Avery, later sexually assaulted a 10-year-old altar boy.
The jury acquitted Lynn of two other charges, including that he had conspired with church leaders to endanger children. But Sarmina declared him a risk to flee, revoked his bail, and sent him straight to prison.
His sentencing hearing unfolded in a courtroom crammed with representatives from each of the groups touched by a decade of scrutiny on clergy sex abuse in Philadelphia.
They included prosecutors and investigators, who had long portrayed Lynn as a gatekeeper for the archdiocese.
Evidence they culled from secret church files and produced during his three-month trial showed that Lynn cataloged dozens of abuse complaints between 1992 and 2004. But he was often slow to seek out other victims, share information with accusers, or press the cardinal to remove priests who had been accused of or even admitted abusing children.
Lynn's relatives, friends, and former parishioners also packed several rows in the courtroom, and hundreds more sent letters to the judge, defending him as an undeserving scapegoat for flaws of church leaders.
A half-dozen took the stand and, at times tearfully, described the 61-year-old cleric as a kind, caring priest who mentored young clerics, consoled troubled mothers, rushed to the bedside of the dying and, at least later in his career, was vigilant about protecting children.
"There are very, very few people that we let get close to our children - and Msgr. Lynn is one of them," said Matt Coyne, the father of seven children and a parishioner at St. Joseph Church in Downingtown, where Lynn was pastor from 2004 until his arrest last year. "That is a good man . . . welcome in my home anytime."
Nearly as many courtroom seats were filled by relatives of the former Northeast Philadelphia altar boy who became the central victim the case. The man, now in his 20s, was sexually abused by Avery in 1999 at St. Jerome Church.
Assistant District Attorney Patrick Blessington told the judge that Lynn may have been a good priest, but he was a "criminal" secretary for clergy.
"Of course he did good. Every priest does good," Blessington said. "There is a time for mercy and a time for justice. This is a time for justice. How many opportunities did that defendant have to show victims mercy?"
Recounting letters from victims, Blessington said Lynn had a front-row seat to the horrors of clergy sex abuse when he met with victims. They described being raped or fondled as children; spending years battling addiction, depression, and suicidal thoughts; and their inability to form or maintain relationships.
"He studied it, he saw it, but most importantly, he ignored it," Blessington said.
Lynn's lawyers, Thomas Bergstrom and Jeffrey Lindy, argued that imprisoning him would accomplish nothing. Lynn had a history of community service that he could build on, they said, and had endured years of national notoriety that served as both a punishment and a deterrent - for Lynn and the church.
"As a result of the verdict, his faith is now crowned with guilt. And his guilt is crowned by faith," Bergstrom said. "The lesson learned will make him and the church better for all time."
Sarmina noted the positive portrait of Lynn that emerged in letters she received, but wasn't swayed. "It's not that hard to be good when you don't have to make the tough choices that challenge your values to the core," she said.
The judge said she believed that Lynn had drafted a now-infamous list of suspected and confirmed pedophile priests in the archdiocese in 1994 because he really did want to address the problem of priests abusing children.
But somewhere along the way, she said, his goal shifted to protecting the church.
The judge threw at Lynn a quote from Archbishop Charles J. Chaput, the new leader of the 1.5-million member archdiocese: "Sooner or later, evil always undoes itself. Sooner or later its consequences become too painful for sensible people to bear."
The monsignor, she said, learned to ignore the evil and tune out the victims. He deserved such a stiff term, Sarmina told him, because of "your support and facilitation of monsters in clerical garb . . . who destroyed the souls of children."
Lynn had been jailed in isolation at the city's Curran-Fromhold Correctional Facility since his conviction. He is expected to be transferred to Graterford Prison while he awaits a more permanent assignment.
The sentence marked the end of the trial phase but not of the legal proceedings. Lynn and the archdiocese are defendants in at least nine civil suits filed by alleged abuse victims, including the man assaulted by Avery.
Two other clerics are awaiting trial on abuse charges, including James J. Brennan, Lynn's codefendant, whose case ended in mistrial.
The judge postponed until Aug. 6 a hearing to decide whether Lynn should be free on bail while his lawyers appeal the verdict and a sentence they called grossly unfair.
"Ask any single D.A. or defense attorney inside who lives in this courthouse what a three- to six-year sentence is like for this case and they will laugh at you," Lindy said.
District Attorney Seth Williams said the term was appropriate. "No matter what the sentence was, it wouldn't really be enough for the victims of child sexual abuse," Williams said after the hearing.
Victims' advocates agreed.
"Considering all the kids whose innocence was shattered (or, in some whose lives were lost to suicide), we believe that Msgr. Lynn deserved the harshest punishment," said a statement from Survivors Network of Those Abused by Priests. "Still, this sentence sends a powerful message: Cover up child sex crimes and you'll go to jail."
Terry McKiernan, the president of the watchdog group BishopAccountability.org, said the sentence was important because it could embolden other prosecutors to pursue similar cases.
"For the first time we have a model for prosecuting the two crimes of clergy abuse," he said, "the clerical abuse of children and the enabling of that abuse by church officials."
Contact John P. Martin at 215-854-4774 or firstname.lastname@example.org, or follow on Twitter @JPMartinInky.
Inquirer staff writer Julie Zauzmer contributed to this article.
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