Hall filed a lawsuit against the Pentagon and Welborn for injunctive relief to prevent such unconstitutional abuses.
In response to his lawsuit, Hall has been assaulted by fellow soldiers and threatened on blogs with being killed by friendly fire. (There have been some allegations, not substantiated to my knowledge, that Pat Tillman's death by friendly fire may have been the result of his outspoken atheism.)
Welborn, who was initially misidentified in the lawsuit as Paul Welbourne, was tracked down via his MySpace page, a visual monstrosity which says that he is a member of the "Department of Eternal Affairs," his primary occupation is "Bible Study," he has a Bachelor's Degree from Tennessee Temple University with a major in "Pers. Evangelism" and minor in "Biblical Worldview," and he attended Tara High School from 1976 to 1983. (In fairness to Welborn, the heading says that the school information is for "MAJ Freddy & HIS Girl," so the dates probably include "his girl"'s high school career along with his own, rather than indicating that he took seven years to get through high school.)
The U.S. military has had a serious problem with Christian evangelicals who don't understand what freedom of religion means. Earlier this year, the Pentagon Inspector General's office issued a report that officers who appeared in uniform in a recruiting video for Christian Embassy, a group that promotes Bible studies by senior government officials, violated military rules by doing so. Two years ago, evangelical Christians proselytizing at the Air Force Academy led to a review of the Air Force rule for chaplains which says that there can be no proselytizing those of other religious faiths, but it's perfectly acceptable to proselytize to "those who are not affiliated." A lawsuit against this evangelizing was thrown out of court last year, but the rule for chaplains with the double standard was revoked.
More on the Hall and Christian Embassy cases may be found at the Questionable Authority blog, as well as the links in this post.
UPDATE (March 7, 2008): Hall has updated his complaint to include a charge that he has had a promotion blocked because of his unwillingness to "put aside his personal convictions and pray with the troops."
UPDATE (July 10, 2008): The government has filed a motion to dismiss (at the last available moment to do so), arguing that Hall lacks standing to sue and did not take advantage of all available remedies within the military to pursue his complaint before suing.
UPDATE (April 26, 2008): The New York Times has now covered this story. (About time!)
UPDATE (April 28, 2008): Ed Brayton at Dispatches from the Culture Wars asks the question of why Hall had to be transferred out of Iraq for his own safety, rather than the commanding officers telling the troops to leave him alone or be punished.
UPDATE (October 18, 2008): Hall has withdrawn his lawsuit on the grounds that he will soon be out of the military and suspects the case will be dismissed for lack of standing once he's out. A second case filed by Dustin Chalker will continue.