You're right in that it's probably not the best idea for the WH to be leading the charge, but what do you do when the other "news" organizations who should be leading the charge aren't doing their job? What do you do when you repeatedly get punched in the face and those who should be doing something about it don't do anything? Do you stand there and let the beating continue or do you punch back?
MSNBC savages them every night I think, and Daily Show mocks them ceaselessly (along w/ CNN and the other cable channels in general.) Fox is the best at providing the material.
I wouldn't say they are left alone, but, as soon as the WH is out in front making these accusations, it changes the nature of the debate. It becomes a partisan political fight between gov't and the media. The media should be duking it out themselves. Between the cable shows and the blogosphere, there are plenty of people to attack Fox.
The WH said their bit, Fox deserved it (esp if they have commentators on their morning shows calling the president a racist and a Nazi), but they should then drop it publicly. They got the ball rolling, let other forces in the media fight the fight. Its too much of a dangerous precedent otherwise.
W tainted his office so much by the manipulation and corruption of the media, I wish Obama to be better than that.