People are judged everyday. Jesus said that we would be judged on how we judge others. Jesus said that we would be shown mercy if we show others mercy. If I were to judge someone for being a glutton when they overeat at Thanksgiving, I would judging myself- since I have overeaten on Thanksgiving, too. If I were to judge a man for raping and murdering a 7-year-old child, I wouldn't be judging myself, since I have never murdered a 7-year-old child and I have never raped a child (or anyone else). We need judge and juries because there are people who are dangerous and need to be put in prison and kept away from society- to prevent them for harming someone else.
And putting someone in prison for murder is not the same as persecution of Jews, Blacks, LDS, Gays, etc. Those groups, for the most part and as a whole, don't go around harming others. The ones that do harm others are put in prison.