Updated 12:30 p.m.

An article in Sunday’s Times has angered and disappointed a large number of academics and scientists, especially women, some of whom are calling for its retraction and stating that it adds to the problems women face in a still male-dominated field.

“Women are dramatically underrepresented in our field and other sciences, in part because of the sexism and misogyny that this article reinforced,” said a letter to Times editors signed by more than 200 astronomers and physicists.

Their objections were to an article about Geoffrey Marcy, a prominent Berkeley professor and astronomer whom the university’s investigation has found guilty of sexual harassment of students over many years. The writers charged that the article was sympathetic to Mr. Marcy, rather than to the victims, and focused on his apology and excuses, rather than to the violations. They also strongly objected to the inclusion of comments from Mr. Marcy’s wife, who played down what her husband had been found guilty of doing, and to the article’s referring to Mr. Marcy’s “troubles.”

“By overlooking the gravity of Marcy’s predatory behavior,” the letter said, “this article discourages women from speaking out and undermines the safety of students.” (The news website Mashable wrote about the objections earlier this week; and the original reporting on Mr. Marcy’s history of harassment came from Buzzfeed.)

I also heard from other Times readers who were not among those who signed the letter, but who were similarly upset. For example, Julie Rehmeyer of Boulder, Colo., a freelance math and science writer, wrote:

It was entirely inappropriate to interview Geoff Marcy’s wife for this article. The important thing here isn’t any infraction he committed against his wife; it’s what he did to the women he harassed. His wife has no valuable perspective to offer on his harassment, and bringing her into it suggests that this is a domestic issue. She is the least likely person to have seen his inappropriate and harassing behavior or to have a perspective that will enlighten the rest of us.

The science editor, Celia Dugger, said that she considered the larger issues involved in this case important ones, and that her department was continuing to pursue coverage. (A third article was published Wednesday afternoon, reporting that Mr. Marcy was resigning.)

Ms. Dugger told me that the original article was done quickly — in a single day, after the news broke. And, she said, while she considered it essentially solid, there were elements that she would have preferred had turned out differently. The headline, which many objected to, should have emphasized the main information in the article — the harassment and university action — rather than the apology. And, she said, she would have made the commentary from Mr. Marcy’s wife shorter and less prominent, but she thought it was acceptable to include because it was a part of getting his side, and because it was interesting.

She strongly defended the article’s author, Dennis Overbye, who has been criticized by those who say he was too friendly with Mr. Marcy to write an objective article. And she said that The Times stood by its article, and that there would be no retraction.

“It was an evenhanded, straightforward news story,” Ms. Dugger said. And while Mr. Overbye had indeed written a profile of Mr. Marcy, there is no reason to think he was biased toward him or incapable of writing a fair article, she said. She pointed out that the profile was not a puff piece but a balanced look at Mr. Marcy and his ideas.

“Because you write a profile of someone, it doesn’t make you his personal buddy,” she said.

She also called Mr. Overbye, whom she described as a fair-minded and highly accomplished reporter, “one of the great jewels of the science desk, and our pre-eminent writer about the cosmos.” Mr. Overbye was a finalist for the Pulitzer Prize in 2014 for explanatory journalism for his work on the race to discover the Higgs boson or what some have called the God particle.

The original Times article lacked some of the telling detail of the university’s report, she said, because — as he scrambled to report on Saturday — Mr. Overbye did not have access to confidential documents.

My take: This situation is considered newsworthy largely because it involves a prominent scientist at a major university. However, the victims in this situation are clearly not Mr. Marcy and his wife but rather the young female students who were preyed upon by a professor. Sexual harassment, which often comes at the hands of a person with more power than his victims, does real harm. And within the sciences, women already face gender-related obstacles in their careers.

The headline, which does so much to set the tone, was not inaccurate but it tilted toward the perpetrator’s point of view, rather than that of the victims. As Ms. Dugger notes, it should have focused — as the article’s first two paragraphs rightly did — on the wrongdoing and the university’s findings, rather than the apology.

I also agree with the critics that Mr. Marcy’s wife’s commentary was out of place in this news article; as readers have noted, she’s hardly a credible source here. That was particularly objectionable because Mr. Marcy’s response and his wife’s defense were given priority over the voices of female scientists and even over quotations describing the university’s censure. Meanwhile, the victims’ experiences were given shorter shrift.

In other words, for a number of reasons, the focus in this initial article was off. If The Times continues reporting on the larger topic (a worthy one), there should be no further emphasis on the “troubles” of harassers.