First of all, I'd like to say I'm quite impressed both sides of this debate are conducting themselves like adults. Secondly, the answers to your questions above are "no." This article answers your questions using DoD regulations and court precedent: Prayer and Religion in the Military | American Center for Law and Justice ACLJ. It's worth the read to answer questions like the ones you asked. This being said, your hypothetical squadron commander still doesn't have to "check his faith at the door." The article explains all the nuances and restrictions...