Symbolism, Imagery, Allegory
The lightning rod in "The Lightning-rod Man" is basically a symbol of human fear. The lightning-rod salesman holds up his rod and says, hey, I can control the wrath of the gods, be afraid. And the narrator says, no way, your lightning-rod is stupid, no one can control the wrath of the gods. And the lightning-rod guy gets angry and attacks, plunging, as the narrator says, "his tri-forked thing at my heart." (4.70)
Then the narrator says, "I seized it; I snapped it; I dashed it; I trod it." (4.71) Irrational fear and superstition is broken and sundered; the bad guy is banished, enlightenment banishes lightning. Triumph!
Of course, lightning-rods actually do work to protect homes from lightning. Melville's science seems kind of shaky (not for the first time; in Moby Dick he argued that whales were fish rather than mammals.) If Melville is denying the efficacy of lightning rods, he's promoting superstition, not fighting it, like anti-vaccine proponents who claim they're fighting for science.
So, rather than a symbol of the triumph of knowledge over human fear, you could see the destruction of the lightning rod as a triumph of confused ignorance. But oh well; even great authors can make mistakes sometimes.