I keep talking to people about this, and they keep responding, "Oh, Obama probably did it because they don't have enough evidence to win in civilian court." And that's not true, and it's not even the point. The point is, George W. Bush pushed the dangerous idea that the 9/11 attacks were acts of terror by states, not individuals - and that was the rationale for invading Iraq. Trying the 9/11 attackers in military tribunals is saying the Bush-Cheney doctrine was right, and lays the groundwork for bipartisan support of pre-emptive attacks:

The Justice Department's restoration was among the most important tasks facing the Obama administration: The Bush administration's political appointees had dismantled the hiring practices that allowed career attorneys to make hiring decisions, and gave more weight to ideological conformity than legal expertise. The result was a Justice Department where incompetent ideologues with political interests in mind were given more power than career attorneys concerned with upholding the law. Michael Mukasey began the process of de-politicizing Justice after he replaced Alberto Gonzales; Eric Holder has continued it.

In light of this, I think Andrew Sullivan's observation of the conflict between Rahm Emanuel and Holder over the prosecution of the alleged September 11 conspirators is especially important:

But whatever your view, this must not, it seems to me, be a politicized decision. It should be a matter of justice. And to go from a Rove-driven Justice Department to an Emanuel-driven Justice Department is not the change most of us who supported Obama wanted to see. Or believe in.

I'm not interested in going from a Justice Department whose behavior is driven by Republican political interests to one whose behavior is driven by Democratic political interests. That's going nowhere at all. Retreating on the decision to try Khalid Sheikh Mohammed in civilian court won't undo all the important changes the administration has made to the Justice Department, but it would reinforce the idea that the Department is a political fiefdom rather than an entity that exists to enforce the laws of the United States and secure the rights of its citizens.

A separate point is that Republicans won't budge on Gitmo anyway, no matter what Lindsey Graham says, so Emanuel's choice isn't even smart politics.