The atheist needs to
make his/her own place in the military, just as conscientious objectors have found. It isn't his/her place to try to change it and make the majority bend to the will of a minority. If an atheist has a distaste for the vastly religious feelings of service personnel, he/she should walk away from signing those enlistment papers. The military makes many accommodations for different religious groups, including having pastors and imams, etc. available to those who need counseling other than Christian based.
Surprisingly, there was just recently a judicial decision made in one of our cities where one atheist complained about a nativity set up on public land (possibly local government property, not sure). Normally, all it seems to take is one to complain and the local communities have taken down Christian items or plaques rather than use budget funds to fight something; however, in this instance, that community was willing to fight it in court. The court decided that as long as the nativity wasn't a LIVING nativity (using live persons and animals) it could stay in place. FINALLY......sanity ruled.