There have been some good explanations of the Fr. Murphy case in regards to the Congregation of the Doctrine of the Faith and how then-Cardinal Ratzinger was involved in the case. I think though that Jimmy Akin has the clearest and best presentation of the Fr. Murphy case I have seen. He lays out the facts as we know them along with the Church’s process and timeline of events. He also points out areas where the handling of the case could prudentially be criticized.
The hysteria that the New York Times generated in it’s piece which could be described as a “Pope hunt” go so far beyond the evidence that it is hard to see other than malice involved. Though Jimmy Akin also charitably addresses this aspect.