The US Military has the duty to uphold and defend the Constitution. There is a Constitutional right to freedom of religion. There can be no restrictions on religious beliefs in the military. We were taught that our beliefs cannot be dictated by the military, but our actions can.
Clearly, the shooter in Fort Hood is disturbed and arguably criminally insane.
Back to the OP, serious or not, one of the first statements by one general or another was that he was worried about backlash. Backlash would be just as bad as the original crime, maybe worse. Justice will happen. Give it time.
P.S. The military is so sensitive to religious freedom that it allowed for the Church of Satan to be put on dog tags. I always wondered what prayer a chaplain would say over the body of such a soldier.