What about if the Metrons didn't care and Kirk destroys the Gorn ship? Later it turns out to have been gallantly defending Gorn space against an (accidental) Federation invasion. Then the Feds look like both the heavy and the fool at the same time. Or they catch up and the Gorns beat the Enterprise, becoming more encouraged by the victories in space and at Cestus?
Both options would likely have been worse than what happened when the Metrons interfered. Its refreshing to see a plot where a larger power got involved in a fight between 2 "lesser" groups and actually helped both sides out.