Congress this week passed HR 4310, the 2013 National Defense Authorization Act, when the House and Senate both agreed to the version of the bill set out in the Conference Committee Report. The 1590-page bill contains provisions impacting military chaplains and conscience rights of members of the military.
Section 508 of the Act (adding 10 USC Sec. 8039) creates the position of Chief of Chaplains in the Air Force.
Section 533 of the Act protects conscience rights of military members and chaplains. It provides:
SEC. 533. PROTECTION OF RIGHTS OF CONSCIENCE OF MEMBERS OF THE ARMED FORCES AND CHAPLAINS OF SUCH MEMBERS.
(a) PROTECTION OF RIGHTS OF CONSCIENCE.—
(1) ACCOMMODATION.—The Armed Forces shall accommodate the beliefs of a member of the armed forces reflecting the conscience, moral principles, or religious beliefs of the member and, in so far as practicable, may not use such beliefs as the basis of any adverse personnel action, discrimination, or denial of promotion, schooling, training, or assignment.
(2) DISCIPLINARY OR ADMINISTRATIVE ACTION.—Nothing in paragraph (1) precludes disciplinary or administrative action for conduct that is proscribed by chapter 47 of title 10, United States Code (the Uniform Code of Military Justice), including actions and speech that threaten good order and discipline.
(b) PROTECTION OF CHAPLAIN DECISIONS RELATING TO CONSCIENCE, MORAL PRINCIPLES, OR RELIGIOUS BELIEFS.—No member of the Armed Forces may—
(1) require a chaplain to perform any rite, ritual, or ceremony that is contrary to the conscience, moral principles, or religious beliefs of the chaplain; or
(2) discriminate or take any adverse personnel action against a chaplain, including denial of promotion, schooling, training, or assignment, on the basis of the refusal by the chaplain to comply with a requirement prohibited by paragraph (1).
(c) REGULATIONS.—The Secretary of Defense shall issue regulations implementing the protections afforded by this section.God and Country Blog has more on Sec. 533.
As reported by Politico, last month the White House threatened a veto over various other provisions in the Senate version of the bill, including limitations on transfer of prisoners from Guantanamo Bay. (Statement by Executive Office of the President.) However, National Journal now reports that a Presidential veto is highly unlikely.