Regarding Raymond Davis in Pakistan, & the NY Times
It seems obvious that people in Pakistan - public and government - knew that Davis was CIA. A confirmation in the Times would affect that belief/knowledge - one word: Baloney.
What was news that was not treated with skepticism was The President's statement that Davis was "our diplomat." This was patently euphemistic; additionally, "our diplomat" would have been employed by the U.S. government, not "a contractor."
Regarding Times relations with the government: Remember Judith Miller & Iraq.