The hacker more than likely won't be punished for his exploit, and honestly, should he? What he did could easily be construed as civil disobedience─"hacktivism", as it were. Put simply, it's our fault(excluding I, of course; I haven't downloaded the ROM, but I will share the blame)─the downloaders. Like it or not, your individual actions(as in those who download, but don't buy) are what's actually to blame. Would you blame Smith & Wesson for making a gun that killed someone dear to you? No. You'd blame the shooter. All the same, no raindrop ever thinks it's responsible for the flood.
So, by that logic, why the hell does it matter who did what? It's our responsibility as Chrono fans to mitigate Square Enix's damages from hereon.