Secular troops cannot win wars against religious enemies.
The Normans captured Pope Leo IX in 1053.
Soviet Russian troops overran many nations.
North Vietnam's Viet Cong won over South Vietnam and the US military.
Religious adherence is no guarantee of victory against secular troops.
That being said, in my four years in the USAF I saw no religious discrimination against atheists or agnostics or any other religion (other than in basic training where Christians got to go to church on Sunday and everybody else had to clean the barracks).
Atheists are America's most despised religious minority, yet they are overrepresented in the US military, and underrepresented in the prison system; and not known for flying planes into skyscrapers.