The Harper's article is behind a paywall, but Alina Stefanescu has more:
Sharlet describes a current "civil war" between the "majority of military personnel, professionals who regardless of their faith and lack thereof simply want to get their jobs done" and the "small but powerful movement of Christian soldiers concentrated in the officer corps".What men such as these have fomented is a quiet coup within the armed forces: not of generals encroaching on civilian rule but of religious authority displacing the military’s once staunchly secular code. Not a conspiracy but a cultural transformation, achieved gradually through promotions and prayer meetings, with personal faith replacing protocol according to the best intentions of commanders who conflate God with country. They see themselves not as subversives but as spiritual warriors—“ambassadors for Christ in uniform,” according to Officers’ Christian Fellowship; “government paid missionaries,” according to Campus Crusade’s Military Ministry.
Sharlet cites the Officers' Christian Fellowship as a key player in the "fundamentalist front" of the officer corps, with 15,000 active members at 80 percent of military bases and a recent annual growth rate of 3 percent.Founded during World War II, OCF was for most of its history concerned mainly with the spiritual lives of those who sought it out, but since 9/11 it has moved in a more militant direction. According to the group’s current executive director, retired Air Force Lieutenant General Bruce L. Fister, the “global war on terror”—to which Obama has committed 17,000 new troops in Afghanistan—is “a spiritual battle of the highest magnitude.” As jihad has come to connote violence, so spiritual war has moved closer to actual conflict, “continually confronting an implacable, powerful foe who hates us and eagerly seeks to destroy us,” declares “The Source of Combat Readiness,” an OCF Scripture study prepared on the eve of the Iraq War.
Update: Here's a Democracy Today video of Sharlet and Mikey Winestein, who has been dealing with this problem for the past several administrations...