When you come right down to it, Khan had a super weapon that he could only use once, a beat up starship that he likely didn't have enough people to repair and maintain.
Also, assuming that he did not destroy the Enterprise in the first encounter, Kirk would have told Starfleet Command exactly what was going on. So Khan would have been hunted by more than a training ship full of cadet, but the main fleet.
Whatever he was going to do, he wouldn't have had much time.
The Reliant wasn't a whale probe -- V'Ger -- Narada -- supership, getting close enough to Earth to credibly threaten it with the genesis torpedo (or any Federation Member) would have been unlikely.