President Obama signed into law Wednesday a defense bill including a "conscience" provision (Blade file photo by Michael Key)

President Obama signed into law Wednesday a defense bill including a “conscience” provision (Blade file photo by Michael Key)

President Obama signed into law a $633 billion package of major Pentagon budget legislation on Wednesday that includes a “conscience” provision prohibiting troops for being punished for their beliefs as he maintained the language “will not alter” the rights of gay service members.

In his signing statement, Obama identifies the conscience provision as one of many parts of the fiscal year 2013 defense authorization bill with which he disagrees — calling it “an unnecessary and ill-advised provision” — but says he’s received assurances from the Defense Department that its implementation won’t permit discriminatory actions or interfere with military discipline.

“Section 533 is an unnecessary and ill-advised provision, as the military already appropriately protects the freedom of conscience of chaplains and service members,” Obama said in the signing statement. “The Secretary of Defense will ensure that the implementing regulations do not permit or condone discriminatory actions that compromise good order and discipline or otherwise violate military codes of conduct. My Administration remains fully committed to continuing the successful implementation of the repeal of Don’t Ask, Don’t Tell, and to protecting the rights of gay and lesbian service members; Section 533 will not alter that.”

A bipartisan group of House and Senate lawmakers agreed to include the provision, known as Section 533, as part of the conference report for the defense legislation. At the time, most LGBT groups called the language disheartening, but determined it would have no substantive impact  on gay service members. However, the American Civil Liberties Union had strong objections to the language, saying it could lead to claims to discriminate and to opt-out of anti-harassment training.

Ian Thompson, legislative representative for the ACLU, said Obama’s interpretation of the “conscience” provision is “a welcome step” and the Pentagon should ensure implementation of the provision is consistent with that explanation.

“Providing this explanation of how Section 533 will be implemented by the Department of Defense was a welcome step from President Obama,” Thompson said. “Going forward, it is essential for DOD to ensure that no accommodation of religious belief or conscience can result in discrimination or harm to others.”

The provision is a watered-down version of an amendment inserted into the House version of the bill by outgoing Rep. W. Todd Akin (R-Mo.). The House language gave even greater leeway to troops and military chaplains and had more anti-gay overtones, saying the U.S. military must accommodate service members’ beliefs concerning “appropriate and inappropriate expression of human sexuality.” The conference report ultimately tamed this language in addition to omitting another provision found in the House bill that would have prohibited same-sex weddings on military bases.