First, we're not talking about the desktop here, we're talking about services. Open source provides much better quality for services. It is frankly appalling to me to see the government relying on Microsoft services given the quality and reliability and security of open source alternatives--not to mention the lower cost.
Second, the biggest obstacle to a standardized Linux desktop that everyone can use and rely on is the lack of a big player in the market willing to invest in one. Imagine if the government took even a fraction of the money it spends on Windows desktops, and spent it on developing a standardized Linux desktop instead. Isn't that exactly the sort of coordination problem that governments are supposed to solve?