And that whitewash is not just to defend the national government, but to defend the parties.
I believe this is exactly the reason that the founders didn't want to have a party system. Some of their choices (like the original make up of the senate) I believe were specifically to prevent this.
Further, the entire goal of having strong state governments and a weak federal government was to prevent these kinds of crimes.
For the very reason that the federal government will not prosecute itself, a strong federal government is bad. (Principle agent problem.)
Can you imagine if states were doing extraordinary rendition and torture? Highly unlikely. While at the same time, for a real war, there would be no problem fighting with a bunch of state militias banding together (and it would cost us a lot less... much of our problem is due to the adventurism of our permanent military-- hard to justify keeping it around if you aren't constantly finding wars to start, er, fight.)