The thing that makes this story confusing to many people is that there are multiple overlapping contexts in play here.
1. Glenn Greenwald is attempting to hold Kevin Poulsen accountable as a journalist for holding back information relevant to the story and for failing to disclose his ties to other actors who are directly involved in the story.
2. Greenwald is attempting to establish when Lamo began working for the government in this case, and is using parts of the transcript released so far to show that it was probably much earlier than Lamo claims.
3. He's also attempting to show that it's quite likely that the inhumane treatment being afforded to Pfc. Manning is intended to coerce him into implicating others in his criminal activities whether the facts and the law support that implication or not.