why might the narrator's knot of cruelty be important to the story?

The use of metaphors involving natural things—a "stream of love" and "seed of destruction"—fits with the natural world's prominent role in this story. The narrator describes the tensions in his relationship with Doodle using the thing that they are able to connect the most over: nature's beauty. In this description, there are some traces of guilt; the narrator feels guilty about the way he treated Doodle, because now he tells this story in retrospect in full knowledge of what that meanness will lead to,

"There is within me (and with sadness I have watched it in others) a knot of cruelty borne by the stream of love, much as our blood sometimes bears the seed of our destruction, and at times I was mean to Doodle."