The big difference is that today's judgments have a legal rite. People should be judged with dignity, which was not always the case at that time, and condemnation must be evidence-based, which was not always respected either.
Another difference is that today there is no judgment based on supernatural situations, as was the case of the Witches of Salem. For a judgment made under the aegis of democracy, crime must have motives that can be substantiated. Finally, people who are tried today have a broad right of defense, which was not the case in the Middle Ages.