I think of the Principia Discordia as "How to Deactivate Your Monotheism Programming 101." I wouldn't mind having it around as a holy book, but it's probably not where the meaty stuff lies for Pagans who've been at it a while. I imagine someone in an intense situation like boot camp might prefer meatier stuff. Although really, I the Pagans I've spent the most time with don't typically find their paths most easily with words or books, maybe partly because of the recognition of immanence/experience as valuable. Possibly that's part of what has made the struggle for a pentacle option on military graves and non-Pagan desecration of the first defined ritual space on a military base such a big deal for us?
The pattern of behavior that this guy dealt with is definitely familiar -- dominionism has gained a worrisome hold in the military in some parts of the US in the past decade or so, and it needs to be addressed head on. That a non-Christian was discriminated against in the military was 99% unsurprig to me; it's happened rampantly before to people of many creeds/religions/even Christian sects. That an atheist used FSM humor to gain some kind of social acceptance was also, say, 95% unsurprising. So what I found most interesting was that the disfavored-flavor of the week by the military was an atheist, because I assumed that they'd see far more easy acceptance than a Pagan or a Muslim.