Yes, of course, the American legal system is about due process. And that's what is happening in this case. It is the job of Obama's attorneys to defend Obama, because he is the defendant in this case. Since he is the sitting POTUS, rightly or wrongly, it is the job of a U.S. Attorney to defend him. U.S. Attorneys work for the DOJ. There is nothing unusual about the DOJ weighing in on this case. That's their job.
This questioning of the DOJ's intentions is just beyond ridiculous. If you were a defendant, you would expect your attorney to do everything he/she possibly could to defend you, including attempt to have the case thrown out. That's standard procedure. It's not out of the ordinary.
I am not sure that it is ridiculous. Why then was there a Saturday Night Massacre if every instruction of the president to the Department of Justice is to be considered legitimate?
Was it inappropriate for both Attorney General Richardson and Deputy Attorney General Ruckelhaus to have resigned rather than execute President Nixon's instructions? I don't think so; clearly, it was inappropriate behavior for the president to insist that the Attorney General fire the special prosecutor.
Why was it improper? I think it was because President Nixon was trying to use the Department of Justice both to protect himself from Mr. Cox's investigation and to subvert justice. Attempting to use the DOJ as an instrument to personally protect oneself seems to me to be precluded from presidential powers, and even an impeachable offense.
Is it also inappropriate for Obama to use his office to defend his personal eligibility? I certainly find it questionable behavior at best, and I think that the DOJ's Inspector General (or a special prosecutor :-) should take a look at this.