BlackFive

Shadow Government has an analysis of the piece, that he thinks explains how the Rolling Stone author got access to the general and his staff:

 If you read the Rolling Stone article carefully, you can see that the reporter, Michael Hastings, has woven three stories together. One story is the story of General McChrystal trying to keep up morale in a tough war with his troops thinking he is too worried about civilian casualties and he is forcing them to accept too many risks as consequence. This is also the story of McChrystal feeling under time pressure from Washington. I bet this is the story Hastings pitched to McChrystal's staff and the story McChrystal thought was being reported.

The other two stories are the ones that caused the problem, he says:  the one the reporter really wanted to write (about how the COIN strategy was doomed), and the one he got to write by fortune -- based on comments in a bar in Paris.

The clear context of those Paris-bar remarks is the 'shore-leave' atmosphere that comes when you take people who have been under the pressures of war and command, and put them in a bar with beer for the first time in Lord-knows-how-many months.  I think the decision to let him tag along to the bar, coupled with this is the key fact about how the article got written:

How much time did you spend with McChrystal over the month?
Another strange journalistic twist. The Icelandic volcano happens, and so my two-day trip turned into this month-long journey following General McChrystal and his staff around from Paris to Berlin to Kabul to Kandahar and then back to Washington, D.C. 

So, he was introduced in an unguarded moment when "Team America" was blowing off stress; and then he got to tag along with them because of the volcano.  That explains how he got inside the 'circle of trust' so easily and completely.

Lesson learned:  letting him come to the bar was the problem.  That was the key error in judgment.  They obviously did it because they only expected to have two days with him, and this was a time when everyone would be together to talk.  It was a terrible idea, though.  After they met him in that environment, it would have been easy to think of him as 'one of the boys' and let him tag along wherever.  They lost the professional detachment in the first moments, because they were introduced to him as a friend, in a social setting where they knew they were permitted to blow off steam.