Key plot points
The protagonist is living on a planet populated by a race of small, logical humanoids. They live in harmony with each other, and apparently have never had the sort of strife humanity has had. They also have the trait of being very literal in their understanding of things. They don't grasp metaphor or allegory the way a human being would.
One day, a rocket ship lands on the planet. The protagonist meets the man in the ship. The new arrival is a religious missionary, who has come to the planet to preach the word of God, and convert the indigenous population. The protagonist develops an almost immediate dislike for the arrival, and I believe tries to convince the other man that he should leave, and that he'll just cause trouble. The missionary is, IIRC, somewhat disdainful of the chiding.
The story proceeds with the missionary setting up roots, building a church, and slowly converting the alien creatures. I recall the aliens' understanding of things making it very difficult for them to grasp the ideas behind faith, the wondrous, and so on. It causes great strife among them. The protagonist becomes increasingly concerned about what is happening.
Events take a tragic turn when the protagonist learns that the aliens have planned to test out the knowledge they have gained from the preacher. Specifically (IIRC) the idea of resurrection. I believe the protagonist, understanding the literal nature of the aliens, sees the danger and tries to save the missionary from what he has wrought. The alien beings overpower them in numbers, though. I believe the protagonist is captured, while the missionary is dragged out of the church and then crucified.
The story closes with one of the protagonist's closest friends among the aliens coming to him and (IIRC) freeing him from the church or wherever he's being held.. He tells the protagonist he needs to go to his own ship and flee. All that has happened has torn apart his society, and it is no longer safe for the protagonist to stay. He also understands that the missionary will not be coming back to life, and that they have committed an act of evil for the first time in their history.
Chronology and other Info
No idea on the timeframe of this one. I'd say no later than the 1970s. It sticks in my mind this one is fairly well-known/something of classic. I just can't remember the title or author for the life of me.