No, you're not too dense to see the issue here. I'll give you two reasons, but there are more:
(1) The New York Times does not have operatives on IM sessions with the people in charge of protecting military data in order to convince them to hand over archives wholesale and indiscriminately.
(2) The New York Times doesn't later publish that data so indiscriminately that it takes a crowdsourced data mining effort simply to figure out whether informants have been compromised by the disclosure.
That is kind of a weak argument there, one might easily ask
"If a reporter with the NYT had an IM session with someone who had access to really explosive data and that someone wanted to share it,..." You're saying the NYT would counsel them for that the good of the country they shouldn't share it?
If Ellsberg contacted Sheehan with an IM and offered to send over the Pentagon Papers in '72 you think that Sheehan would have said, "No thanks, that is secret data even though it says the Government has been lying about the war." ?
I'm not convinced. Given the challenges the prosecution is facing with Manning I'm left wondering what evidence the government has that he was an operative or that Wikileaks was anything more than a opportunistic journalistic contact.
Your second claim is that the NYT doesn't publish indiscriminately. But you are trying to argue a possible behavior for a situation that didn't exist. Lets say for the sake of argument that the source was Manning, and that rather than Wikileaks he chose to dump the data on someone at the NYT, then suppose that the NYT spent several weeks going over that data with various understaffers, and the threat of someone else breaking the story came up.
Now are you going to argue that the NYT wouldn't just run with it at that point? How about if in all the weeks of looking they had yet to find anything that would hurt/compromise an innocent third party? Do you know the NYT that well? And unlike 1972 where they were constrained by how many pages of newspaper they could print, on the web you can print everything now and get those clicks early and often.
Given that the NYT has released comparably classified material in the past (I've heard one argument that the state department communications were actually a lower grade classification but cannot find a source for that), and probably still has lawyers on staff from the resulting court cases that caused, its easier for me to believe they would have run with the story.
(1) The New York Times does not have operatives on IM sessions with the people in charge of protecting military data in order to convince them to hand over archives wholesale and indiscriminately.
(2) The New York Times doesn't later publish that data so indiscriminately that it takes a crowdsourced data mining effort simply to figure out whether informants have been compromised by the disclosure.