Of course there may be more to it than that.

Jane Mayer's piece on this subject is very informative.  Here's a relevant excerpt:

At the White House, Emanuel, who is not a lawyer, opposed Holder's position on the 9/11 cases. He argued that the Administration needed the support of key Republicans to help close Guantánamo, and that a fight over Khalid Sheikh Mohammed could alienate them. "There was a lot of drama," the informed source said. Emanuel was particularly concerned with placating Lindsey Graham, the Republican senator from South Carolina, who was a leading proponent of military commissions, and who had helped Obama on other issues, such as the confirmation of Supreme Court Justice Sonia Sotomayor. "Rahm felt very, very strongly that it was a mistake to prosecute the 9/11 people in the federal courts, and that it was picking an unnecessary fight with the military-commission people," the informed source said. "Rahm had a good relationship with Graham, and believed Graham when he said that if you don't prosecute these people in military commissions I won't support the closing of Guantánamo. . . . Rahm said, `If we don't have Graham, we can't close Guantánamo, and it's on Eric!' "