The marginalization of Christianity in a military becoming more and more hostile to religion has left the chaplains feeling muzzled—and they now face same-sex couples coming to them for marriage counseling. The chaplains still get to wear crosses on their collars, so they worry even more about those Christians in regular uniforms losing the First Amendment freedom of religious expression that they volunteered to defend.

This year: An Idaho Air Force base removes a painting called “Blessed Are the Peacemakers” because it references a Bible verse. The Air Force yanks off You-Tube a video tribute to first sergeants because its statement, “God created a first sergeant,” is “highly suggestive of the Book of Genesis in the Bible and has Christian overtones.”

Also this year: An Army Reserve training brief on hate groups declares that evangelical Christians and Roman Catholics are extremists as dangerous as al-Qaeda. A commander tells a chaplain to “stay in your lane” when he offers spiritual advice about the military’s exploding sexual assault problem.

Last year: A superior tells an Air Force major to remove from his desk the Bible he had kept there for 23 years. An Army lieutenant colonel instructs his subordinates to recognize the “religious right in America” as a domestic hate group like the KKK and Neo-Nazis. An Army master sergeant with 25 years of service faces punishment for serving Chick-fil-A sandwiches at his promotion party.

Two years ago: Christian prayers banned at veteran funeral services in Houston’s National Cemetery. Bibles temporarily banned at Walter Reed Army Medical Center. A Christian cross banned from a military chapel in Afghanistan. A chaplain called into his supervisor’s office and chewed out for closing a prayer with the words “In Jesus’ name.”

Coincidence that all these incidents occurred recently? About 80 military chaplains who gathered in South Carolina for a three-day conference last month didn’t think so. George Washington established the military chaplaincy, but Doug Lee, a retired Army chaplain who achieved the rank of brigadier general, told attendees, “You are in the military in a new era.”

The marginalization of Christianity in a military becoming more and more hostile to religion has left the chaplains feeling muzzled—and they now face same-sex couples coming to them for marriage counseling. The chaplains still get to wear crosses on their collars, so they worry even more about those Christians in regular uniforms losing the First Amendment freedom of religious expression that they volunteered to defend.

“We are at war,” said Chaplain Thomas MacGregor, a U.S. Army colonel. In June 2009, MacGregor bucked the trend by invoking Jesus’ name and proclaiming His resurrection during a prayer at the official Normandy ceremony honoring the 65th anniversary of D-Day. Several chaplains turned down the assignment, MacGregor said: “Be as wise as a serpent and as harmless as a dove … that is the rule of the thumb I give to my junior chaplains.”

This May, frustrated with the weight of evidence, Coast Guard Rear Admiral William Lee broke rank, throwing out his prepared text at Washington’s National Day of Prayer event (see video below).

“They expect us to check our religion in at the door—don’t bring that here,” Lee said. “Leaders like myself are feeling the constraints of rules and regulations and guidance issued by lawyers that put us in a tighter and tighter box regarding our constitutional right to express our religious faith. … Pray that we will be able to weather the storm.” Lee received five standing ovations.

Capitol Hill lawmakers are taking notice. In June, Rep. John Fleming, R-La., successfully inserted into a Defense spending bill an amendment stating military personnel will have freedom of conscience and will not be disciplined for their religious beliefs. At the chaplains’ conference Doug Lee commented on that: “Isn’t it tragic that we have to have a special paragraph that would insist on your First Amendment rights which are clearly spelled out already? … That’s where we are.”

Last December Congress passed a similar amendment to safeguard the religious beliefs of service members. But President Barack Obama, when he signed the larger bill into law, said the protections were “unnecessary” and “ill-advised.” Six months later the Obama administration has refused to issue regulations to enforce the protections. At a congressional hearing this spring, Defense Secretary Chuck Hagel seemed to be unaware that the protections were in the law.

The Obama administration issued a statement on June 11 saying it “strongly objects” to a new religious liberty amendment: It would have a “significant adverse effect on good order, discipline, morale and mission accomplishment.” The Administration did not object to an amendment offered last month by Rep. Jared Polis, D-Colo., that would create atheist chaplains. That amendment lost, but 150 House Democrats voted for it.

How bad is the military environment? Reports of the influence of Mikey Weinstein, who met with officials at the Pentagon and has called religious proselytizing “a national security threat … sedition and treason … spiritual rape,” are probably exaggerated. But Major John Sackett, an Air Force chaplain, told me at the conference that Air Force chaplains like himself have “fear of retribution. … I often ask, ‘Will what I need to say now actually get me in trouble?’”

Complicating this are legitimate concerns that in the past some Jewish, Muslim, Hindu, Buddhist, or other members of the American military have felt the pressure that minorities often feel. But, as Michael Horowitz of the Hudson Institute has put it, evangelicals in many ways are the new Jews of American society, facing discrimination of the kind Jews felt two generations ago.

John Wells, a former Navy commander turned lawyer who represents the master sergeant facing discipline for serving Chick-fil-A at his promotion party, said, “The problem is this case is the tip of the iceberg. I’ve got people calling me all the time saying, ‘I am a chaplain and my prayers are being censored,’ or ‘I am being told if I state my opinion on something that I am going to get hammered.’”

Sackett, the Air Force chaplain, traces this climate of intimidation to confusion about the law: “You are free to pray however your conscience dictates in any situation because that’s the law. … Commanders don’t know that anymore. So many of them actually think it is illegal to talk about Jesus. The commanders are well-intentioned, but they are also not interested in any lawsuits.”

Sackett and his commanding chaplain plan an officers’ training session regarding constitutional law and the free exercise of religion. But even chaplains are bewildered: New ones often ask Sackett if they can offer Bible verses or pray while counseling. Ten years ago, he says, base commanders would often announce upcoming religious events and chaplains would often open and close command level staff meetings with prayer. Not anymore.

Some confusion stems from the military’s own dizzying array of press releases about what is permitted. An Air Force statement this spring said service members could “express their personal religious beliefs as long as it does not make others uncomfortable.” Many chaplains wondered who would be deciding what is uncomfortable—and would this definition change over time?

The Pentagon then said service members could evangelize but not proselytize. That kicked off debate over the differences between evangelizing and proselytization. While chaplains at the conference agreed that coercion has no place in Christian faith, they worried that complex definitions of theological terms would have a chilling effect on discussion. They also discussed reports that the Army’s new definition of resilience has removed the word “spirituality” from the attributes needed for a soldier to overcome adversity.

Evangelical denominations face a hard choice: If they pull their support of chaplains because new rules don’t allow them to represent Christian belief, the gap will be filled by groups with liberal theology. Sackett said, “One of the reasons I am still in is I am afraid who might take my place.” But he may not get a chance to stay: “I think a time is shortly coming when chaplains who speak out on moral issues and on issues of community standards are going to be told go find a new job,” said Chuck Williams, an Army chaplain based in Hawaii.

Moral advising has long been one role of chaplains. On October 21, 1778, George Washington issued an order in which he called “purity of morals … highly conducive to order, subordination, and success in an army.” That is why Wells, the naval commander turned lawyer, fears the repercussions of a military without a moral check: “You know the old saying that there’s no atheists in the foxhole? Well God help us if all we have in foxholes are atheists.”

The chaplains also say the assault on religious liberty in the military, if allowed to stand, could expand to society at large. The military has often been a touchstone for cultural change: “It is just a matter of time before these same challenges are going to come to the local church,” said one chaplain who asked not to be identified because he had received direct orders from his commander not to talk to the media. “You have your head in the sand if you think that you are protected behind the church.”

Despite uncertainty, new chaplains are still entering the fray: The Presbyterian and Reformed Commission on Chaplains has approved 13 new chaplains so far this year. One of them, Ted Hamm, thought about joining the chaplaincy six years ago when he graduated from seminary, but the timing wasn’t right. Hamm ministered at a PCA church in Sarasota, Fla., but never lost his sense of calling to minister to teenagers leaving home for the first time to join the military and wondering what life is all about.

Last year, Hamm, getting close to the cut-off age of 42, filled out the 57-page application and was accepted. He left the June conference with the sobering realization that some in power “oppose what we do and what we believe,” but he said he has no regrets about joining: “My faith helps me to have a really big view of God and a peaceful calming view of his sovereignty in every situation. We have Christ on our side and we have God on our side and nothing can take that away.”

Hamm is more concerned about getting into shape so he can pass the physical requirements during his 13-week chaplain training school set for this fall. A personal trainer who goes to Hamm’s church is putting him on an exercise regime that includes running on an elevated treadmill while wearing weighted vests. He will have to run two miles within 18 minutes and do 35 pushups and 35 sit-ups in two minutes each, and he also wants to gain the respect of his future soldiers by running stride for stride with them even though he will be twice their age—even if that means jumping out of airplanes with the 82nd Airborne.

“That would be awesome,” Hamm said.

Copyright © 2013 God’s World Publications. Used with permission.