However, I would wager that the CEO would have to have intentionally and actively cooperated with the criminal act; merely benefiting from it indirectly by running the corporation is insufficient. Hence they indicted the corporation which is directly benefiting.

Even if the CEO was aware and conspiring the prosecutor would still need to prove it. They may not have evidence beyond a reasonable doubt.

All that being said it is possible prosecution was pro-corporate biased and refused to burn down a company. I am not discounting that possibility. Regardless it is difficult to win convictions so it is also plausible this is the best win prosecution believed it could get.