The problem isn't when journalists agree to keep some information off the record to protect a source. It's when doing so fundamentally changes the character of a story or is actually part of the story itself.
What Greenwald outlines is a journalist who is thoroughly compromised. It's gone so far that he's actually part of the story.
Two other similar examples come to mind:
1. When Judith Miller was given false information about Iraq that she used to write pro-Iraq invasion stories, she was using anonymous Bush administration sources. When it turned out that this information was incorrect, she decided to protect the identity of her sources. A real journalist would have realized that the story was: "Bush Official X leaked false information to journalists in order to sell the war to the American people." When a source makes you that much of a fool, you burn them, unless you were a helpful collaborator.
2. When Robert Novak outed Valerie Plame as a CIA agent, he protected his source. At this time, Scooter Libby was peddling this information on behalf of Vice President Cheney's office. This was in retaliation for her husband, Joe Wilson's, release of information dismissing the Iraq/Niger Yellow Cake story that the US used as a reason to go to war. However, it turned out that it was Tim Russert (a longtime member of the DC press establishment) who had passed along the leaked Scooter Libby information to Novak. Tim Russert covered the Valerie Plame story for years before anyone knew he was the reason for her outing. And Russert failed for years to use his inside knowledge to report the true story to the American people. This led to Scooter Libby being able to take a minimal charge of obstruction of justice and ultimately a sentence commutation from George Bush.
So this isn't so much about keeping notes or a transcript. It's about a member of the press with the truth at their disposal, but choosing to hide it for some reason. My guess is he's writing a book and would like to keep some information proprietary, but considering the case that Greenwald levels, some sort of response is appropriate.