"The issue is over how he should be punished."

Eh, no, that's not what the issue is about. The article states explicitly that no reason for the reversal was given (yet), but it seems to be about the extent of 'interstate commerce'. I.e., a purely technical legal point, having nothing to do with the material matters in the case.

But they are related. If the conviction was upheld, he could be punished criminally with jail time. With the conviction overturned, Goldman can still go after him civilly for breach of contract which is relatively similar to a fine.

"Relatively similar"? No it's not. Criminal conviction or not, GS could still sue, albeit that the proof would be easier. Either way, I don't understand the relationship between your post and mine, or the whole point that is being made here.

I wonder if Teza even used the code Aleynikov took with him. If they didn't, would he even face civil penalties?

Punitive damages maybe, plus maybe contractual obligations on damages in case of breach. If they didn't use it, and if a civil case was purely based on damage caused (two big ifs), I don't think there would be much of a (civil) case, no, because there needs to be causality between the breach and the damages, which then there wouldn't be.

Still he could be done on theft of trade secrets & breach of contract and Teza could see what GS had tried what wored what didnt which is worth a lot.