Even if he violated confidentiality agreements, wouldn't that be a civil violation instead of a criminal one? Why is the federal government prosecuting what should be a civil case?
GS wanted an example made, so they got the FBI to prosecute. 8 years inside makes for a really big stick to wave in front of the rest of their programmer base.
Unfortunately for them, the court has ruled that the statute in question didn't apply, so the ruling has been reversed. Assuming double jeopardy applies, he can't be prosecuted (by the government) again for the same acts. I think that GS could still sue for breach of contract, but their damages would presumably be limited to actual harm done wouldn't they?
They could be but they could seek punitive damages and/or treble damages. Honestly, in the case of getting sued by GS costs are probably the biggest factor.