There is a fierce battle going on over what kind of a CIA director Barack Obama should appoint, when he should close the prison camp at Guantanamo, and whether there should be a full scale investigation (and possible prosecution) of the torture advocates in the Bush administration.

If you’ve only been reading The New York Times, you’re probably aware of these battles—but almost everyone you have seen quoted about them has similar points of view. Most of the Times’s sources don’t think that anyone who formulated or acquiesced in the current administration’s torture policies should be excluded as a candidate for CIA director, or prosecuted for possible violations of criminal law.

The story on the front page of Wednesday morning’s New York Times provides the most recent and the most dramatic example of this syndrome. The story, by Mark Mazzetti and Scott Shane, noted that John O. Brennan had withdrawn his name from consideration for CIA director after liberal critics attacked his role in the agency’s interrogation program, even though Brennan characterized himself as a “strong opponent” within the agency of harsh interrogation techniques. Brennan’s characterization was not disputed by anyone else in the story, even though most experts on this subject agree that Brennan acquiesced in everything that the CIA did in this area while he served there.

Brennan’s self-defense was followed by a quote from another ex-CIA man, Mark Lowenthal, who claimed that Brennan’s downfall “sent a message that ‘if you worked in the C.I.A. during the war on terror, you are now tainted,’ and had created anxiety in the ranks of the agency’s clandestine service.”

“I was aghast reading this,” said Scott Horton, a professor of human rights law at Hofstra and a contributing editor at Harper’s, whose blog was instrumental in framing the opposition to Brennan’s appointment. “The Times doesn’t even do a reasonable job of presenting the conflicts—their principal source today was John O. Brennan. They have not reached out to the other side. It looks like Mark and Scott have decided that it’s payback time for a couple of their sources at the agency.”

Horton also disputed the idea that an investigation of agency abuses would “would demoralize the line officers of intelligence and the military.” The people saying that are “very very skillfully pointing to the interrogators as being the targets—because they know they would not be the targets. The people who would be the targets are policy makers like [Cheney chief of staff David] Addington, who have the same ability to attract sympathy from the public as cockroaches. I’m not sure that the early part of the story is going to be so embarrassing to the company. There was push back at the beginning; you had pretty high level opposition and Cheney decided to cram it down, which is why they went to get that Department of Justice memo” authorizing the torture of prisoners.

Horton added that people in the CIA say Brennan is “absolutely correct he wasn’t responsible for shaping this policy; but when he suggests he was a vigorous opponent, they laugh.”

Asked by Full Court Press about Horton’s suspicions that the piece he had co-authored was payback for his sources at the CIA, Mark Mazzetti replied, “What am I going to say to that? It’s like absurd.”

The Times piece also framed the debate as a contest between CIA veterans and the “left flank of the Democratic Party.” But the only opponent to the Bush administration’s torture policy quoted in the piece was retired general Paul D. Eaton, who oversaw the training of Iraqi forces for the Army in 2003 and 2004.

Eaton, who is one of a group of forty retired admirals and generals opposed to torture, told the Times, “This administration has set a tone problem for the military. We’ve had eight years of undermining good order and discipline.”

I asked Mazzetti if he thought Eaton and his fellow retired generals and admirals regarded themselves part of the “left flank” of the Democratic Party. The Times reporter replied, “I wouldn’t want to comment on that. I think our piece pretty much stands for itself.”

Charles Kaiser is the author of The Gay Metropolis and 1968 in America. He has been media editor for Newsweek, a member of the metro staff of The New York Times, and a reporter for The Wall Street Journal, where he covered the press and book publishing. To learn more, visit charleskaiser.com.