The Army Court of Criminal Appeals just handed down an opinion on this a few days ago, rejecting the claim, asserted by Sgt. Abdullah Webster as a defense to charges of "missing movement by design and disobeying a superior commissioned officer." A few highlights:

1. "Appellate defense counsel now assert the military judge erred in accepting appellant's plea because he 'did not freely plead guilty' and appellant's 'guilty plea was irregular and not freely given because the Islamic scholars ... forbade [defendant] from deploying to Iraq [and] doing so would condemn [appellant] to hell." The court says no: "It is irrelevant that appellant missed movement or failed to obey the orders of his superior commissioned officers based on religious motives."

2. Defendant also argues that the federal Religious Freedom Restoration Act provides a defense, presumably because of his view that

Based upon the advice given to me by Islamic Scholars ... the conclusions were: 1. Consensus was that this [sic] no Muslims are permitted. 2. Muslims are not allowed to kill another Muslim except under three conditions . . . . Given the religious ruling, any combatant role I undertake would jeopardize my belief and place me in an unfavorable position on the Day of Judgment.

RFRA provides that, when the federal government substantially burdens a person's religious practice -- for instance, by requiring him to do something that his religion forbids -- the person is entitled to an exemption (even when the law is generally applicable, and doesn't single out religious people for special burden) unless the government shows that applying the law to the person is the least restrictive means to serve a compelling government interest.

The court says no: Even if the order burdened defendant's religious practice (which the court assumes for the sake of argument),

The Army has a compelling interest in requiring soldiers to deploy with their units. As the Supreme Court has said, “[i]t is ‘obvious and unarguable’ that no governmental interest is more compelling than the security of the Nation.” The Army’s primary mission is to maintain national security by fighting and winning our nation’s wars. The Army cannot accomplish this primary mission if it cannot deploy, in a state of military readiness, the various units into which it is organized. Giving soldiers the option to decide selectively whether they wish to participate in particular military operations would undermine the readiness of all units to deploy, and thus compromise the Army’s mission and national security.

In this case, the Army furthered its compelling interest in the least restrictive manner possible. Although the Army required appellant to deploy with his unit, the Army made numerous allowances for him. The Army afforded him the opportunity to request relief as a conscientious objector. The Army gave him the right to request reasonable accommodation of his religious practices. Finally, although apparently not required to do so by any regulation, appellant’s commander generously allowed appellant to deploy with his unit in a non-combatant role....

As the Supreme Court has stated, “to accomplish its mission the military must foster instinctive obedience, unity, commitment, and esprit de corps.” ... “The inescapable demands of military discipline and obedience to orders cannot be taught on battlefields; the habit of immediate compliance with military procedures and orders must be virtually reflex with no time for debate or reflection.”

Sounds quite right to me. I should also add that the Supreme Court held in Gillete v. U.S. (1971) that people weren't entitled to a religious exemption from the duty to serve in the military, beyond what was provided by the limited conscientious objector exception (which applies only to those who object to all military service, rather than to those who refuse to fight in what they see as "unjust" wars). Gillette was decided during the era when the Court viewed the Free Exercise Clause as providing a presumptive right to religious exemptions; the Court later reversed that position, but the Religious Freedom Restoration Act basically reinstated the Gillette-era religious exemption doctrine as to the federal government, so Gillette would still be good precedent as to RFRA cases (though for some reason the Army Court of Criminal Appeals didn't cite it).