LGBT rights supporters are expressing disappointment with “conscience” language included in the final version of major Pentagon budget legislation, and although views on its potential impact are mixed, most say the language won’t have a substantive change on current military policy.

A bipartisan group of House and Senate lawmakers made public on Tuesday their agreement for the fiscal year 2013 defense authorization bill, a $633 billion proposal that sets policy for the Pentagon, continues pay for troops and provides funding for military programs.

But these lawmakers also agreed to include a watered-down provision along the lines of an anti-gay measure included in the House bill by outgoing Rep. W. Todd Akin (R-Mo.). That provision was understood to mean service members would be allowed to harass their gay colleagues and that military chaplains could refuse to minister to them simply by saying to do so goes against their religious beliefs.

The language in the conference report, listed under Section 533, is divided into two parts: the first says service members can’t be punished for their beliefs so long as they don’t violate the Uniform Code of Military Justice, the second says chaplains can’t be punished for refusing to perform a ritual contrary to their religious beliefs.

The section isn’t as overtly anti-gay as the House language — there’s no mention of “human sexuality” or sexual orientation — and says service members can still be punished if they act or speak out on their beliefs.

Lawmakers were expected to take up the legislation by the end of this week. House Armed Services Committee Chair Buck McKeon (R-Calif.) said during the conference that he was hopeful for a vote Thursday.

Ian Thompson, legislative representative for the American Civil Liberties Union, was among those offering the strongest objections to the “conscience” language, saying passage could lead to “claims to discriminate, not only against lesbian, gay, and bisexual service members, but also against women, religious minorities, and in the provision of health care.”

“It could reopen longstanding prohibitions against harassment, could lead to claims of a right to proselytize other service members as well as civilians in occupied areas, and could lead to claims of an opt-out from providing health care or participating in anti-harassment training,” Thompson said.

One conservative group is also claiming victory. Tony Perkins, president of the anti-gay Family Research Council, expressed satisfaction over inclusion of the “conscience” language in a statement.

“We are happy to see that Congress has included language in the Department of Defense reauthorization bill that will protect the conscience rights of chaplains and service members,” Perkins said. “This language provides for the protection of the First Amendment rights of all our men and women in the Armed Forces.”

But the “conscience” provision is one small part of the defense authorization bill aimed at continuing funds for the Pentagon and paychecks for U.S. troops. Moreover, the provision was included in exchange for dropping another provision in the House bill that would have prohibited same-sex marriages on military bases.

Progressives have reason to celebrate because the final report includes a provision in the Senate bill offered by Sen. Jeanne Shaheen (D-N.H.) to expand health coverage to cover female service members seeking abortions in cases of rape and incest. Previously, the Pentagon would only provide an abortion in the event the mother’s life was in danger.

Furthermore, other LGBT advocates didn’t express the same sense that “conscience” language would have significant impact.

These advocates are echoing the sentiment of Rep. Adam Smith, top Democrat on the House Armed Services Committee, who told the Washington Blade during a news conference on Tuesday that while he personally doesn’t support the language, it won’t have a substantive impact on the military because it’s consistent with current policy.

“I think that’s current law,” Smith said. “You can’t punish someone based solely on their beliefs. It has to be actions. That’s current law. I didn’t think that this language needed to be in it. If you ask me, what the one thing I would take out of this bill, if I could, that would be the one thing I would take out of this bill. Now, it’s significantly neutered, if you will, to the point where I don’t think it’s going to be a problem, and I’m going to support the bill, but that is a provision that I did not support.”

Among the groups saying the provisions would have no effect are the Human Rights Campaign, OutServe-SLDN and the Center for American Progress.

Michael Cole-Schwartz, a Human Rights Campaign spokesperson, called the provision “unnecessary” in the wake of repeal of “Don’t Ask, Don’t Tell,” but also “meaningless.”

“While it’s bad, it’s also meaningless in a lot of ways,” Cole-Schwartz said. “We were successful in making sure an extension of DOMA wasn’t included and it’s not clear that this language, while unfortunate, will have meaningful consequence for service members.”

Allyson Robinson, executive director of OutServe-SLDN, called the inclusion of the language “disheartening” — especially because it comes on the second anniversary of “Don’t Ask, Don’t Tell” repeal — but says it won’t create any new policy for the Pentagon.

“Indeed, no service member or chaplain is ever punished for his or her religious beliefs unless he or she acts on those beliefs in a way inconsistent with military law or good order and discipline,” Robinson said.

But Robinson also said the appearance of the language in the defense bill should serve as a cautionary tale.

“The fact that provisions such as these could make their way into this bill is an indication that the gains we have made are fragile and that we must remain ever vigilant even as we look toward the work ahead of us needed to achieve full equality in our military,” Robinson said.

Crosby Burns, research associate on LGBT issues for the Center for American Progress, also shared the sentiment that nothing new would happen if the “conscience” provision became law.

“Based on the conference reports language, I believe that it essentially reiterates existing freedoms and protections that service members and chaplains already have,” Burns said. “Obviously, it sets a dangerous precedent because it’s based off language in the House bill that was intentionally crafted to allow people to discriminate against openly gay service members, so obviously that’s cause for concern, but based off the existing language, we believe it doesn’t actually change anything in terms of the substantive policy.”

The White House is staying mum on the conference report provision. A spokesperson didn’t respond to a request for comment after it was made public.

In May, the White House issued a Statement of Administration Policy saying the Obama administration “strongly objects” to the conscience language as it appeared in the House bill along with the provisions barring same-sex marriage from taking place on military bases.

Denying the passage of the provision would have no impact, ACLU’s Thompson drew on the White House objections to the House language while condemning the provision found in the conference report.

“Earlier this year, the White House conveyed its strong objections to the original House-passed language based on how the provision would affect ‘all personnel-related actions based on certain religious and moral beliefs, which, in its overbroad terms, is potentially harmful to good order and discipline,'” Thompson said. “Those serious concerns have — despite initial reports to the contrary — not been resolved by this conference report language. Rather, they are magnified.”

But the White House Statement of Administration Policy doesn’t go as far as a veto threat over the conscience provision if the final version of the bill includes this provision.

Asked whether a veto is necessary, Thompson said the ACLU has already called on Obama to veto the defense authorization bill over an unrelated provision related to detainees at Guantanamo Bay, but hasn’t yet determined whether to include the “conscience” provision as another reason to veto the bill.

“The ACLU, as part of a broad coalition of human rights organizations, is already recommending a veto of the legislation based on its Guantanamo detainee transfer prohibitions,” Thompson said. “We are exploring whether to add this provision as another reason we would recommend a White House veto.”

The complete language of Section 533 of the bill follows:

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.