Double jeopardy applies here doesn't it? You don't get to keep prosecuting people for one act until one of the cases sticks: You have to pick one breach of the law, or bundle a bunch of them into a single prosecution, and go to court on that basis don't you?
IIRC, double jeopardy doesn't stop both criminal and civil charges from being filed for the same offense (it only applies to being criminally charged multiple times)?
You're right (I think), so GS could go after him for breach of contract and/or copyright infringement but not any of the criminal offences that were originally available to them (including the copyright related ones).
Given that their return might be limited to their provable losses & that they'd have to demonstrate those in court I suspect that they'll probably decide it's not worth the effort. The guy has already spent a year in prison after all & they've successfully demonstrated to all their other employees that GS will go for the maximum possible sentence if any of them transgress in the future, which was probably the main point of the whole exercise in the first place.
Double jeopardy only applies to being tried for the same crime twice. It doesn't prevent you from being tried for a different crime that you committed simultaneously with the one you were acquitted of.
You can be acquitted of murder and then tried for conspiracy to commit murder; you can be acquitted of "economic espionage" and then be tried for criminal copyright infringement because they're two separate crimes, though committed in the same act.
Double jeopardy applies to the same act, not the same crime. You cannot be tried for the same act twice if the case is fully resolved (i.e., it ends with a plea or a verdict or an appeals court renders a decision that "prejudice" shall apply.)
This is why prosecutors always overcharge: if they undercharge, they are foreclosed from seeking a conviction on the more serious charges once the case is resolved (whether they win or lose).