Not being armed in such an environment is insane. I spent most of a decade in Iraq and Afghanistan, and unless I was on US bases with vastly better security, was armed in any situation where it was possible (there were a couple exceptions in Afghanistan and they were horrendously stupid.)
(Not religious, and not a "security contractor" -- we ran wifi and satellites and such -- but zero interest in being kidnapped and beheaded in a crappy video like one of my high school classmates. Never had anything bigger than a .30cal, and generally low profile vs big armored trucks, but also never got kidnapped.)
Given the lack of US QRF in the conflict areas of Iraq today, the case for every humanitarian or commercial entity being armed is even stronger now.
Some form of neutral, armed-for-self-defense entities for both commercial and NGO services would make a lot more sense than relying on foreign governments. While I love a lot of what MSF does, they have been criminally negligent in securing their personnel in places like Afghanistan.