I think you're right that many of the machines in mission control are Sun based. At the very least it was an OS that I wasn't completely familiar with when I worked in there a few months ago during the SpaceX mission.
It's real money, but it's not like it's flushed into space. It's paid out to scientists, engineers, and administrator in the form of salaries. NASA seems bad because that number seems really high but when you compare it to the rest of the government it's a tiny drop in the bucket