Jacob Sullum outlines the president's Gitmo dilemma:
Instead of vetoing a military spending bill that forbids the use of taxpayer money to transfer prisoners from Guantanamo to the United States for trial, he may issue a signing statement declaring that the restriction unconstitutionally impinges on his authority as head of the executive branch and commander in chief of the armed forces. The Times says it is "unclear whether the administration would actually carry out a detainee transfer despite the restrictions, or whether it would merely assert, as an abstract matter, that Mr. Obama had the authority to do so."
Much better, I believe, to veto the bill. That's the president's strongest and obvious constitutional option.