What is the main lesson in "the man to send rain clouds"?

One possible lesson you could draw from the story is that seemingly incompatible belief systems ultimately point to the same truth. On the face of it, it would seem that the gap between Roman Catholicism and the indigenous Pueblo culture can never be bridged. And Leon appears to feel that way too, which would account for his reluctance to inform Father Paul about Teofilo's death. Leon wants the old man to receive a burial according to traditional native rites; Father Paul's involvement will interfere with Pueblo traditions.
Yet in actual fact, Leon's concerns are misplaced. By sprinkling holy water on Teofilo's dead body Father Paul actually contributes to the effectiveness of traditional Pueblo burial rites, ensuring that big clouds of rain will soon be on their way, replenishing the earth with new life. Although Father Paul may not fully understand the part he's played in Teofilo's funeral ceremony, he has inadvertently shown that Roman Catholicism and traditional indigenous religion can co-exist, not least because they both partake of the one underlying truth that unites us all in death as well as life.