Here are some Jewish people being massacred in Lisbon's main square. Notice the people up front. As key members of the Portuguese Inquisition, Portuguese Jesuits and other mendicant friars searched out hidden Jewish communities, who were massacred upon discovery. This went on from 1531 to 1773. The fact that the Portuguese Jesuit characters in this film were witnessing Buddhists doing to Christians what Jesuits did to Jews in Portugal was either intentional or unintentional irony. Scorsese never lets on.
It's a very well-made movie, but the main character is not believable as a 17th century Jesuit. Every aspect of his character bleeds with modern thinking, and there's no getting past that for me.