Sure they do, to put public pressure on Apple. I don't think anyone knows exactly what happened here, but we can be sure that Sony's version is not the whole story.
Time will tell. If this does represent a new Apple policy, Barnes and Noble and Amazon's readers should both be removed in the near future. If that doesn't happen, I think we can presume that there is something hanky about Sony's statement.
I article implies that their source is not just Sony. It says:
The company [Apple] has told some applications developers, including Sony, that they can no longer sell content, like e-books, within their apps, or let customers have access to purchases they have made outside the App Store."
This quote implies that there are other application developers that have been told the same thing. What are these other applications? Who told the NYTs about these other applications (including Sony's)? I don't really know. But, it doesn't necessarily mean that Sony is the source.