Building rockets/ballistic missiles, is something the "bad guys" already know how to do, so I seriously see no reason why the Linux part of that should be any secret.
f.ex. the Danish Open Source project "Copenhagen Suborbitals" - which are hard working at building rockets, and have launched a few already, publish documents, detailing how they've build the different rocket types they built - it's all available for download right here: http://www.copenhagensuborbitals.com/
It's sad they felt the need for such IMHO unneeded secrecy, and about Linux even - which has NOTHING to do with the ballistic missile part, which isn't even a secret either.