Why not send a torpedo, nuclear bomb or some other weapon?
All the 72 torpedoes going off together damaged the Vengeance only slightly. It was still in better shape than the Enterprise, being able to manoeuvre to San Francisco and all. And that was the best arsenal they had.
They couldn't fire. Spock said as much. I guess Kirk could've pulled a Janeway, and fired the torpedoes manually, but dying from it. I am not sure what the reaction would have been if Spock screamed Marcuuuuuuuuuuuuuuuuuuuuuuuuuuus! and aligned with Khan out of rage.