Update: The ACLU has likewise opposed the religious protections in the bill, which a local article called a “needed balance.”

The Congressional conference committee has sent the 2013 National Defense Authorization Act (NDAA) back to both houses of Congress for a vote.  (It is reportedly expected to pass, and to be signed by President Obama.)  The conference committee report includes expanded abortion coverage, a restriction on Guantanamo detainee transfers, and religious liberty protections for US troops.  The religious liberty protection language is not precisely what the House had passed (as opposed to the Senate, which passed none), but it is substantially similar:

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.

The committee explained the result of their negotiations this way: 

The conferees intend to accommodate the beliefs of service members, but preserve the authority to take disciplinary or administrative action for speech or conduct that violates the [UCMJ], including actions and speech that threaten good order and discipline.

The original House text specifically addressed homosexuality and did not include the caveat.  The compromise seems intended to give the military leeway to prosecute conduct already prohibited by the UCMJ, while simultaneously giving explicit protections to troops’ religious beliefs.  To the point, “actions and speech that threaten good order and discipline” are already, and have always been, proscribed by the UCMJ.

The clause protecting chaplains who refuse to conduct homosexual ceremonies was also included.  The House abandoned their section prohibiting the use of military chapels for homosexual ceremonies.

The legislation directs the Secretary of Defense to create regulations “implementing the protections” in the law.

The Chaplain Alliance for Religious Liberty praised the move, with retired Chaplain (Col) Ron Crews saying

This is a significant step in assuring that all of our military personnel, including chaplains, can continue to serve and maintain their religious beliefs or moral convictions without fear of retribution…

By contrast, the Secular Coalition for America — which includes American Atheists and the Military Association of Atheists and Freethinkers — has called for Congress to vote down the bill, because it codifies protection of “discrimination:”

The amendment would allow service members to discriminate against other service members based on religion.

Section 533 of the [NDAA] will allow chaplains and other members of the Armed Forces to discriminate against LGBT service members free from disciplinary action.

The press release demonstrates its own ignorance, since the Department of Defense already (legally) discriminates against the “T” in “LGBT” by banning “transgender” individuals from service.  The DoD does not need this legislation to do that.

Beyond that, it is unclear what the Secular Coalition actually thinks people could do that would constitute “discrimination” (or what they called “religiously-motivated bullying”).  The intent of the law, obviously, is to codify protections for what was already previously allowed.  After all, that’s precisely why other critics said the law was “unnecessary.”

In the end, it seems an effort has been made to protect the religious and moral consciences of US troops, even as social mores change the culture in which they serve.

As to the critics, this law, should it be signed, will be no less valid than the one that repealed DADT.