I'm sure a vanilla linux-distribution is as easy an target as a windows box, if not even easier.

But why don't they use some hardened (grsecurity,selinux) kernel + http://linux-ima.sourceforge.net/ + a default forbid MAC policy + remote logging.

I can't see how this attack vector could be used against such a system.

These are deadly drones. It is probably a lot more work than using a plain windows box. But these machines can kill people. I thought the Military would use state of the art software security system.