It shouldn’t be much of a surprise that State Department spokesman P.J. Crowley has resigned his post in wake of his too-candid assessment of the incarceration conditions of suspected Wikileaker Private First Class Bradley Manning.

Last Thursday, Crowley told a panel at MIT that the Pentagon’s treatment of Manning at the Marine bring at Quantico, Va., was “ridiculous and counterproductive and stupid.”

The very next day, President Obama told reporters that he felt Manning’s confinement conditions were “appropriate.” His answer telegraphed a problem for Crowley. “I’ve actually asked the Pentagon whether or not the procedures that have been taken in terms of his confinement are appropriate and are meeting our basic standards,” Obama said, suggesting some of those procedures were to protect Manning’s safety. “They have assured me that they are.”

Manning is currently being held alone in his cell 23 hours a day, and was reportedly being stripped naked at night before being given a tear-proof smock for sleeping. Free speech advocates are shocked, and, as I wrote last week on TIME.com, concerned over Obama’s record as the most aggressive prosecutor of suspected government leakers in U.S. history.

Those advocates have wondered whether the penchant for secrecy in the Obama administration comes from the President, or those around him. Obama’s statement on Manning, followed by Crowley’s resignation, seem to suggest some of this comes from the President himself.

In a Sunday statement announcing his resignation, Crowley sought to clarify his remarks. “The unauthorized disclosure of classified information is a serious crime under U.S. law,” he said. “My recent comments regarding the conditions of the pre-trial detention of Private First Class Bradley Manning were intended to highlight the broader, even strategic impact of discreet actions undertaken by national security agencies every day and their impact on our global standing and leadership.”

Secretary of State Hillary Clinton thanked Crowley for his service and announced that he will be replaced by Michael Hammer, who transferred from the National Security Council to Foggy Bottom earlier this year.