The university has opened two new residential colleges this semester, one named for a black Yale Law School alumna and civil rights leader, Anna Pauline Murray, and the other for Benjamin Franklin. The latter decision, too, has left many people “a little miffed,” said Vivian Dang, a Hopper College junior. “It’s another old white guy being honored.”

Calhoun, who graduated from Yale in 1804, is not vanished from the campus. His name and likeness remain in the stonework above a couple of archways at Hopper College.

A plaque in the courtyard honors the “Renovations of Calhoun College in 1989,” funded in part by “the generosity of S. Roger Horchow, Class of 1950.”

“We’re never taking this down, because he was a great supporter of the renovation,” Prof. Julia Adams, the head of Hopper College, said of Mr. Horchow, a mail-order catalog mogul and Broadway producer. There is still an eight-foot statue of Calhoun high up on the university’s Harkness Tower, too.

Nor has Yale seen its final battle over an icon that some people now find offensive. Last month, the school said it would remove a “problematic” doorway carving that shows a Puritan settler aiming a musket at a Native American, after drawing criticism for simply covering up the gun.

And critics have pointed out that for all the effort Yale has expended on figuring out ways not to honor a 19th century white supremacist, the proportion of African-American students at the university — 8 percent — is about the same as in 1980, a trend that holds at most elite universities. Another 6 percent of current Yale students identify as multiracial, a category that did not exist until 2008.