Everything is virtualized. The software is Open Source, and much of the courseware is available free. The book you still have to pay for, but it's very cool nonetheless.
Lots of the cost has to do with being radiation and temperature hardened. The methods are one-off for programs like this. There is little to stop it from scaling though - it's just a matter of getting the economies of scale.
From the Wikipedia page, the RAD6000 was used in the Mars Rovers. I believe that the Mars Rovers used Java, partly because of static analysis that can be performed on source and object code and partly due to the garbage collection.
I would be shocked if the actual rovers used Java. Perhaps Java is used in the tools used to control them (that send the signals), but not the little guys themselves.
http://en.wikipedia.org/wiki/RAD6000
I couldn't find what language they were working in, does anyone know? Ada?