In short, Shenon finds the gravamen of the case against Rachel to be her implementation of the priorities of her superiors and her failure to follow the agenda of her subordinates.
If the case against Rachel presents a test for Michael Mukasey, my guess would be that both he and she will pass the test, though perhaps not if the New York Times is doing the grading.
JOHN adds: Shenon implies what we have long suspected is the view of many liberals, including many at the Times: that it is the role of federal employees to battle against, and refuse to implement, the policies of Republican administrations. Still, this particular instance borders on the bizarre. The policy which Rachel is being criticized for implementing is Gonzales's effort to crack down on the trade in human sex slaves. It is hard to imagine the Times, or anyone else, criticizing this priority if it came from anyone but Gonzales, or any administration other than that of George Bush.