In a lucky turn of events, Fairness & Accuracy In Reporting talks about the media coverage of the US-backed Afghan corruption: http://fair.org/counterspin-radio/peter-hart-on-syria-and-sarin-dilip-hiro-on-afghan-corruption/
Their guest, Dilip Hiro, had apparently previously written this article on a much more full extent of the US-backed corruption in Afghanistan than anything portrayed by the New York Times: http://www.tomdispatch.com/blog/175677/
Looks like a pretty open and shut case of typical media behavior. According to Hiro in the FAIR interview, it was merely a case of the NYTs providing a positive framework, spin, and red herring from the real debate. I guess that is a very important thing for the NYTs, the ability to present stories that are really quite dangerous, but to do so in a way that cloaks true understanding and true relevance.
Final Conclusion: Although the story garnered at least some media attention, having fully read Manufacturing Consent now I see completely that even though there were a couple of NYTs articles presented on the story, it's still quite within the framework of the propaganda model as compared to the case studies Chomsky & Herman present in the book (even the unbecoming to US power items still got some misleading media coverage in the book), with about the same media coverage as "unworthy victims" and "illegitimate third-world elections" as well as about the same clarity, honesty, and intent.