The controversy surrounds Palistani-born Kaukab Siddique, a tenured professor at the state-funded, historically black college in Chester County.
As the issue first unfolded, the university stood by Siddique and affirmed the right of faculty members to express their views outside the classroom and away from campus -- no matter how controversial the subject matter.
But in a change of course, Lincoln University's president, Ivory Nelson and it's executive vice president, Michael Hill, released a statement on Thursday, calling Siddique's comments on Israel and the Holocaust "insidious."
Affirming the Holocaust as historical fact, the two added that "his statements reflect poorly on the reputation and integrity of Lincoln University."
But the administration also said that Siddique, like all faculty members, was entitled to convey his own views in public forums as long as he does not present them as the views of the university.
As a result, the statement said, it could not "take action at this time based on the content of Dr. Siddique's statement."
Nelson was pressed to repudiate Siddique's comments in a Thursday meeting with four state lawmakers. The politicians had pressed the administrator to condemn Siddique's rhetoric and investigate the process by which he received tenure, back in 1991.
That meeting came two days after the chairman of the Pennsylvania State Board of Education, Joseph Torsella, wrote to Nelson and asked that the school investigate whether Siddique had used school resources to produce his online magazine and, whether his tenure should be reviewed.
Also this week, several Jewish advocacy organizations sent individual letters to the Nelson and were also working on a coordinated response to address the situation.
Siddique made headlines last week when a speech he made on Labor Day in Washington was posted by www.investigativeproject.org  and reported by the Christian Broadcasting Network.
In the footage, Siddique tells a crowd at an anti-Israel rally: "We must stand united to defeat, to destroy, to dismantle Israel -- if possible by peaceful means."
In the same talk, he also refers to the Sept. 11 terrorist attacks as a "Zionist plot."
Siddique, who heads a Baltimore-based organization that promotes anti-Jewish conspiracy theories, has also written that "the Auschwitz 'gas chambers' story has been meticulously analyzed, rebutted and destroyed by critics like Mark Weber, David Irving. Germar Rudolf and Wilhelm Staeglich. These are scholars following the highest levels of scholarship."
The case of Siddique is raising questions about whether there are limits to free speech, and if public institutions can fire employees for private behavior. It also focuses attention on the issue of academic tenure, and whether it affords too much cover for teachers to say and do outrageous things.
The publicity that Siddique has received has also brought to the fore the perennial question of just how the Jewish community should respond to anti-Israel sentiment on campus.
"We've got to apply some kind of pressure," said Adam Kessler, director of the Jewish Community Relations Council, who convened a meeting with representatives of Hillel, the American Jewish Committee, Operation Understanding, the Anti-Defamation League and the Zionist Organization of America. "It's just not something that we can stand for."
In many ways, this situation is different from others that have focused on academic freedom. The controversy around Siddique appears to center on views expressed outside the university setting -- though the ZOA, for one, is citing indications that he has spoken about Israel on campus.
Several sources expressed concern that, if Jewish organizations acted too rashly, the whole issue could be seen through a black-Jewish lens and become a flashpoint for inter-ethnic tensions.
State Sen. Anthony Williams (D-District 8), an African-American lawmaker from Philadelphia, stated: "We don't want this to be just a Jewish issue. It's an American issue."
Williams and State Sen. Daylin Leach (D-District 17), a Jewish lawmaker from Montgomery County, sent a letter to Nelson last week, pressing for more information on the matter. Joining them in meeting with Nelson on Oct. 28 were State Rep. Bryan Cutler (R-District 100) of Lancaster County, State Rep. Lawrence Curry of Jenkintown and State Sen. Vincent J. Hughes (D-District 7) of Philadelphia.
Williams labeled Siddique's comments as hate speech and said that the university -- founded in 1854 and formally associated with the state since the 1970s -- was created as a response to prejudice, not to help perpetuate it.
"We're not on a hunt to get rid of this guy," said Williams, but rather to press Lincoln "to be true to its character."
Williams called the Oct. 28 meeting a "good first step" and said university officials, though defensive at first, appeared ready to engage in a dialogue about freedom of speech and faculty tenure. Williams said he suggested a meeting between Nelson and representatives of various Jewish and other groups such as the National Association for the Advancement of Colored People.
Lincoln University spokeswoman Ashley Gabb acknowledged last week that Siddique has a history of making controversial comments outside the classroom.
She sought to distance the university from Siddique's "personal views," and said that "there is no evidence of his personal views being presented or articulated in the classroom."
She added that Siddique has every right to exercise his First Amendment rights outside of the classroom. She also said that she was a student of Siddique's, and described him as an excellent instructor who "challenged you to learn."
Steve Feldman, executive director of the Zionist Organization of America's Greater Philadelphia District, pointed to a post on Siddique's online magazine, www.newtrendmag.org , stating that, back in September, the professor answered questions on campus about his controversial statements.
While many are hearing Siddique's views for the first time, Barry Morrison, regional director of the Anti-Defamation League, noted that his organization has been tracking the professor's comments for about five years.
Morrison said that Siddique heads a Baltimore-based organization called Jammat Al-Muslimeen, which promotes anti-Jewish conspiracy theories. On Thursday, Morrison sent a letter to Nelson citing reports that Siddique had shared his views on campus.
"We urge you to scrutinize this information and determine how it bears on the concerns we have communicated to you," wrote Morrison.
According to the ADL's website, Jammat Al-Muslimeen rejects Western-style democracy and considers the U.S. government to be under Zionist control.
Morrison has previously asked Nelson to repudiate the instructor's views, but the college president has not done so.
Siddique did not directly answer an e-mail requesting comment. But he forwarded his response to the Christian Broadcasting Network last week, in which he wrote: "When I refer critically to the 'Jews,' I am referring to the current leadership of the 'State of Israel' and to their major supporters, not to the Jewish race as a whole."
In an interview this week with Inside Higher Ed, Siddique invoked academic freedom. He also warned against universities being intimidated by politicians and outside commentators.
"That's freedom of expression going up the smokestack here," he was quoted as saying.
Jeffrey Pasek, a lawyer and First Amendment expert who chairs the board of the liberal-leaning Jewish Social Policy Action Network, said that while Siddique's views are indefensible, the university lacks legal grounds to pursue terminating the educator's job.
That's not because Siddique has tenure, but because he works at a public institution, explained Pasek. While a private employer isn't bound by the First Amendment free-speech rights, a public university is, although it can regulate what is said and taught in the workplace.
In fact, 30 years ago, a group of professors successfully sued Lincoln University in federal court on the grounds that the administration had trampled on their First Amendment rights, said Pasek. The professors had spoken out against a plan to trim the size of the faculty.
In his view, trying to force a concession from the school is not the way to go.
"In a conflict over ideas, good ideas will win out," he said. "This fellow's crackpot thinking has been exposed in ways that have given him publicity, but which also allows the marketplace of ideas to address it. The answer to bad speech is more speech, not suppression of speech."
Feldman said that while he respects the First Amendment, "the fact that people might look to him as a role model is troubling."
The ZOA head, who planned to take part in the JCRC meeting, questioned whether the university would have reacted differently if a professor made questionable comments about, for instance, Muslims or gays.
"We saw what happened last week to Juan Williams," said Feldman, referring to National Public Radio's decision to fire the journalist after he said on a Fox News program that when he's seen passengers on a plane wearing "Muslim garb," he becomes nervous.
Rabbi Howard Alpert, executive director of Hillel of Greater Philadelphia, said that the Jewish community should not press the university to disavow its faculty member.
Instead, he said that Jewish groups should use this episode as an opportunity to develop a relationship with officials at Lincoln. Right now, he said, practically none exists.
"We're going to have to devise a strategy that deals forcefully with the individual, but at the same time, is sensitive to the academic culture of the university," said Alpert. "I have no indication that the university itself harbors anti-Semitic or anti-Israel culture."