It's pretty easy to envision this. Say something he did caused a pallet not to be included on a manifest and it had to go out on another flight when a human at the other end noticed it was missing.
Say something he did caused a war to be lost... if you stretch it far enough then you get to the horseshoe of the courier. It's up to the military to deal with adversity. All the time. They should have procedures and checks in place to make sure this stuff can never happen.
If one bozo in his moms basement can cause hundreds of thousands of dollars in damage or worse they have real problems, and suing the guy that did the damage is the least of their issues.
Oh yeah, obviously any military system that can affect the real world ought to be protected by the best firewall you can get - the AirGap(tm). I'm just describing a mechanism by which changing data can end up costing money in the real world. You could probably really screw up someone's business just by running their printer out of paper.
It probably comes down to time spent trying to track whether or not he did something malicious and other investigative processes necessary. Put a few security experts or a consulting firm on the case for a year and it gets quite expensive. Also if they found out he compromised sensitive information and had to change plans or reschedule something then expenses start racking up.
By the way, I would like to know how could he have made $800.000 in damages. Is this the money spent to make the system more secure?