No they won’t. I promise you. The military and it’s members are required to respect each others beliefs and lifestyles. I have never seen someone be persecuted for something like this. It is admirable that you want to serve your country, and by all means, you shouldn’t let anything stop you. I am an atheist and I have not received any Flak whatsoever yet. We talk about it, and it comes up, but I am treated as an equal. This environment allows others to learn about you, it’s a safe ground for open-minds. I think you should go for it. People will ask you ignorant things sometimes, but don’t let your feelings get hurt… Many times they just don’t know better. I have had people ask me “How do you have morals” or “You are so nice, how can you be an atheist?” This is not meant to be rude, it really is a lack of understanding, so the best you can do is explain to those who will listen.
Go for it :)