Part of the reason that Windows is an approved OS is enterprise support. When you pay for hundreds of thousands of licenses for a product you can demand features. If the DoD went with Debian they would need an entire corps of developers to maintain government specific patches. Ubuntu offers enterprise support but it's from an African country and that is undesirable as you mentioned above.
I've seen government systems running Windows (USA), Mac (USA) but the strangest I've seen is SUSELinux (Germany). I have no idea how they got SUSE approved when Red Hat is more "American" but some agencies don't have to follow the rules.