What needs to be done now is to compare the French penal code with the British penal code and with the penal codes of the other major powers of the period and see what they did and the punishments they inflicted on convicted criminals.
It appears to me that the only country being 'judged' here is France, as well as only Napoleon as head of state. And that judgment is coming from an early 21st century viewpoint and not from a viewpoint of the period. Justice was administered very bluntly and rehabilitation of criminals was not addressed (and it doesn't work anyways, despite what left-wing apologists for criminal behavior maintain).
So, if there is to be a fair judgment here, the other nations should also be looked at and compared with the French penal code regarding trials, incarceration, and punishments.