The Jewish social philosophy class at Yeshiva University was supposed to focus on repentance, but there seemed to be too much to atone for. In the eyes of the students, Bernard L. Madoff had deceived scores of people, turned billions of dollars into dust and ruined many lives. So instead, the graduate seminar of 15 began by debating whether Mr. Madoff’s actions were sins, and whether it mattered that he was Jewish.

One by one, the students in Rabbi Norman Linzer’s class last week wrestled with the headlines and their emotions. Some said Mr. Madoff’s religious affiliation was irrelevant; others worried that his Judaism might tarnish their own, that outside eyes would not be able to see past his faith.

Since Mr. Madoff was charged by federal prosecutors with orchestrating a $50 billion fraud, each day has brought new pain to the nation’s best-known Jewish institution of higher education  word that another familiar charity tied to Jewish causes had been thrust into financial uncertainty, another university family’s savings depleted.

Yeshiva, a campus of about 7,000 students in Upper Manhattan, is grappling with a sense of personal betrayal that extends beyond the $110 million it says it lost in investments with Mr. Madoff, who had been on the board of trustees since 1996. There is resentment; fear of the revival of ugly, old stereotypes; and, after the fall of a favorite son, uncertainty about how Jewish institutions like theirs should choose role models.