I am unaware of Philip Zelikow's broader history, but perhaps if I was better read this wouldn't come as a surprise. Zelikow says that not only did he urge the Principles not to approve a torture program, but all known copies of his dissenting memo were collected and destroyed.
At the time, in 2005, I circulated an opposing view of the legal reasoning. My bureaucratic position, as counselor to the secretary of state, didn't entitle me to offer a legal opinion. But I felt obliged to put an alternative view in front of my colleagues at other agencies, warning them that other lawyers (and judges) might find the OLC views unsustainable. My colleagues were entitled to ignore my views. They did more than that: The White House attempted to collect and destroy all copies of my memo. I expect that one or two are still at least in the State Department's archives.
The Bush Administration knew what they were doing was illegal, and they went about destroying evidence of that fact.