FWIW - I completed 20 years in the Navy and was an atheist the entire time. I don't recall any time I was in where not attending services or not bowing my head was an issue...personally I did not care if it did cause issue with anyone, I wasn't about to cater to the "popular" religion of the day - I was in the Navy to do a job.
Actually I do recall one incident in berthing where we were having a friendly arguement concerning if Batman could kick jesus' ass and vice-versa. The christian believed he won the arguement and walked away...