Become a MacRumors Supporter for $50/year with no ads, ability to filter front page stories, and private forums.
In the link you provided, it only seems to confirm that the data processing servers on Earth are running Linux, it doesn't really seem to speak about the actual spacecraft itself (full quote below). Would be cool to know what kind of OS that runs though.

You might be wondering what kind of computers are used for all of this. Well, high-end servers are now in use, and they were considered fast machines at the time of purchase. But no matter how fast computers are today, they will seem pretty sluggish in 5 or 10 years, and this mission is at least 9½ years long! For this reason, the hardware will be upgraded at least once during the mission. Also, almost all software used is "open source" (include the operating system, which is Linux), meaning the source code is available in case it is ever needed — which is a good thing for a long mission like this.
 
Hmm interesting.
Early Mars missions used VxWorks as the OS. More precisely a Real time OS or RTOS. Very Unix like with a Real Time scheduler.
I suspect the Horizon may use the same RTOS.

Appears to be Nucleus RTOS by Mentor Graphics.
 
Register on MacRumors! This sidebar will go away, and you'll see fewer ads.