That's simply unrealistic. It's a nice theory but if you're the only people using that software, how is it going to be cost effective to take the burden of maintaining it?
Well you have the same problem if the company that supplies the proprietary software goes out of business except that you are usually just flat out screwed. Granted it's unlikely that someone like Microsoft will go out of business anytime soon (but then again I'd say it's also fairly unlikely that Ubuntu disappears anytime soon and even that would leave you with a fallback option of other, similar Linux distros).
If say Windows XP just gets phased out on you that's not exactly cause for celebration either. And of course there's also the advantage that you can at least theoretically check most of the source code of Linux which is probably somewhat relevant in a government setting (a potential NSA cooperation of Microsoft says hi)
