Person or corporation, a case always begins with presumption of innocence and then trying to prove guilt. It should be the same for executives of that company.
I'm not sure if you're speaking from a point of naivety, but the only point at which the presumption of innocence enters into the justice process is when you step into a courtroom.
Everything prior to that - in all your interactions with police, jails, prosecutors, before your day in court, they will all presume guilt, and will treat you like the criminal scumbag that they think you are.
Oh, and most defendants never even get their day in court.
Sure, you’d start with the presumption that the accused didn’t lead organization or that the organization didn’t commit the crime in question, then try to prove otherwise.
That's more subtle to prove though. Negligence and malice, while both resulting in the same outcome, do deserve different punishments. And my comment was coming from a position of "you have to assume negligence before anything worse".
