Religion never justified crime! Infact, majority of the different world views formed through a religious perspective push for good morals amongst humanity.
A quick glance at world news answers "yes." Perhaps a rephrase: when should religion justify crimes, and then, which ones? Even then, the answer will depend on one's biases and how they inform one's understanding of both religion and crimes. Was hiding Jews from Hitler's SS a crime? Yes, but people motivated by faith did it. Who condemns them? Was it a crime to speak against the Third Reich? Yes. Lutheran minister Dietrich Bonhoeffer did--and they executed him for it. Who condemns him? So, did "religion" justify them both? Yes. Enjoy the exploration.
Religion could justify crimes. That is when the crime is against humanity even if it is not against the present generation. This is because that crime, may cause devastation and annihilation of human wellbeing.