McCain's op-ed was just an attack on Obama. It gave no new details; it was trash. Maybe NYT was trying to remind McCain that he promised to run an honorable campaign? Which, unfortunately McCain forgot about.
I heard that the opening line of his submitted op-ed went like this: "Today's situation in Iraq reminds me of when I was a child during the latter days of the Civil War..." Frankly, I think the NYT did him a favor by not publishing.