I believe this may be The Streets of Ashkelon by Harry Harrison.
Synopsis from Wikipedia:
An atheist merchant/trader, John Garth, is the only human on an alien planet where the native Weskers, intelligent but painstakingly literal-minded amphibians, live in what seem to be utopian conditions. These Weskers have no concepts whatsoever of gods, nor religion, nor sin. Garth has been gradually teaching them the scientific method.
One day Garth is surprised by the arrival of Father Mark, a missionary who is intent on proselytizing to the natives. Despite Garth's best efforts to dissuade him, even at gunpoint, the missionary is intent on "saving souls."
Weeks pass and Father Mark has been instructing the Weskers in catechism in their newly-constructed church, and he has recently finished teaching the Weskers about the Crucifixion and Resurrection of Christ. Soon afterwards, Itin, the ostensible leader of the Weskers, approaches Garth about the problem of reconciling the empirical truth of the scientific method with the symbolic truth of revealed religion and asks him to come to the church to debate Father Mark. Once at the church, Garth, who had previously made preparations to leave the planet, sees the Bible open to an illustration and orders the missionary to come with him. Not understanding what's wrong, Father Mark refuses; but before Garth can explain, several natives seize the priest and drag him to a hill upon which is planted a cross. In accordance with what Garth taught them about the scientific method, they are experimentally testing the hypothesis that if they crucify the missionary in accordance with what he taught them about the Gospels, he will miraculously rise from the dead three days later and thereby redeem them.
Three days later, after Father Mark has been buried and the hypothesis disproved, Itin asks Garth what went wrong, and arrives at a simple truth: that the Weskers are now murderers.
This seems to roughly follow what you described.