Servers with archaic configurations are quite difficult to change like that. Besides, I can reasonably assume the NSA, like most major government agencies, uses some wonky, overly complicated rats' nest of a CMS that croaks with/out the www.
The problem I've always had with this is that DNS root levels (., no www) can't be a CNAME - unless there are any DNS gurus in the audience that can point to some alternate configuration I've overlooked.
No, you're right - it's a serious limitation. Ultimately just a trade-off to consider. As with anything, neither is obviously superior.
You can always just serve a redirect to www.example.com. Doesn't have to be a high-powered redundant server or anything (just secure).
We force the www. at work because of DNS limitations.