With the most compelling figure in this Shakespearean tragedy having exited the stage, the university must find a way to honor Paterno's career without diminishing the tragedy that ended it and without further alienating the coach's family.
While there were always going to be sleepless nights for university administrators in a post-Paterno world, the Jerry Sandusky scandal that led to the coach's Nov. 9 firing turned a difficult scenario into a colossal nightmare.
Less than 24 hours after he had said he would step down at season's end, Paterno was dismissed by a board of trustees that believed he had failed to act appropriately after learning that Sandusky, his longtime defensive coordinator, allegedly had molested a young boy.
The board's action, widely perceived as hasty and indelicate, provoked a firestorm of criticism.
Now with his death, just 65 days after his lung cancer was made public and before any face-to-face reconciliation could occur, how will the university choose to answer questions made infinitely more complex by Paterno's death?
Can the Paternos forgive the university and its trustees for the curt and legacy-scarring dismissal?
Will the trustees, who angered the Paternos and alumni by dismissing Paterno over the phone, attend the funeral?
Conversely, if there is going to be a large-scale, televised memorial service on campus, as many believe there should be, would the aggrieved family attend?
And, maybe most significantly - for the long-term health of the university and the Nittany Lions program Paterno transformed - will the family help Penn State reach out to its many alienated alumni and donors?
After a telephone conversation with trustees Sunday, Keith Masser, 60, a Schuylkill County potato farmer who last week became the board's new vice chairman, confronted the rawness of the situation.
Masser said that the board was looking at a "portfolio" of possible Paterno tributes but added that the family's wishes would be respected.
"It's sensitive," Masser said. "We don't want to step in front of the family. . . . We're maneuvering through a minefield to do it appropriately."
The Paterno family reportedly has rebuffed the board's efforts to make amends.
"We understand the anger, the bitterness, and the grief," Masser said. "I'm hoping time will soften that."
Perhaps tellingly, in a lengthy statement released after Paterno's death, the family made no mention of the trustees or - except in the formal name of a charity to which it directed donations - Penn State. (It urged those making donations to contribute to a student-run charity known as Thon.)
In his final interview this month, the ailing coach said he felt no bitterness toward the school that had employed him since 1950, the last 46 sesons as its head football coach.
But little more than a week later, Penn State no longer has an opportunity to make peace with him.
"Sadly, I believe it means that the scar becomes more permanent," said Anthony Lubrano, a 1982 Penn State graduate, major donor, and friend of the Paterno family. "They had the opportunity to do it, and they chose not to. Now, they must suffer the consequences, whatever they may be."
The firing itself took place in a terse and clumsy phone conversation between the coach and the then-vice chairman of the trustees, John Surma. In recent interviews, several trustees, while not apologizing for the firing, regretted the way it was handled.
That incident only exacerbated sensitivities already present because of the child sex-abuse scandal, causing additional outrage among many students, alumni, and donors.
Paterno's wife, Sue, in fact, called Surma immediately after her stunned husband had hung up. "After 61 years, he deserved better," she said before slamming down the phone.
As far as anyone knows, that was the last communication between the Paterno family and the university it served for six decades.
Subsequently, during three meetings aimed in part at assuaging their ongoing concerns about Paterno's firing, president Rodney Erickson assured alumni that the university would conduct some sort of tribute to commemorate Paterno's many contributions.
But Erickson refused to get more specific, saying only that he would sit down with Paterno when the Sandusky crisis quieted. In the third meeting he had with alumni, this one in New York City, one grad blistered Erickson with this question: Did he plan to honor Paterno or was he just awaiting funeral services?
"Is the family upset? Of course," said an athletic department official who requested anonymity. "But there's one thing you need to remember about them. Sue and all five of the kids are Penn State graduates, loyal Penn State graduates. I'd be shocked if they were willing to cause permanent harm to their alma mater."
Joe and Sue Paterno contributed more than $4 million to the school over the years, most of which went to a library that now bears their name. The university's Catholic Center also bears Sue Paterno's name.
Trustee Michael DiBerardinis, Philadelphia deputy mayor for environmental and community resources, said that what came through in the trustees' Sunday conference call was "a deep sense of loss and grief . . . particularly the folks who were close to Coach Paterno and who either played for him, worked directly for him, or just knew him as a friend.
"There's a real interest in responding to the family's needs right now," he said. "It's important that the university and the board really pause here and recognize his accomplishments and distinguished history."
Contact staff writer Susan Snyder at 215-854-4693, email@example.com, or @ssnyderinq on Twitter.