Superman saved the human race from annihilation and was ready to come out in the open (hence Lois saying "welcome to the planet"). The Enterprise defeated Khan, Admiral Marcus was dead, and there is renewed optimism for the future. How did the heroes lose exactly?
Kirk was the one that led the Vengeance back to Earth, and released Khan from his cell. Kirk's crew got Khan on board a ship he had "inate knowledge of", as Spock said, lining him up to take over the Vengence, which Khan then used to kill thousands of people ... yeah, they prevented Marcus from starting a war with the Klingons, but it was at great cost - I wouldn't call it a victory, and Kirk all excited for his new five year mission at the end of the didn't jive to me, in light of the destruction his enemy had caused - a man he released from a jail cell - most people, no matter if they stopped the "bad guy", would be dealing with the feelings of guilt over the deaths the villain had caused, especially since they had captured him successfully, but then let him go. I would think Kirk would be questioning himself, wondering, "I wonder what would have happened if I had actually just turned Khan over to Marcus - would the admiral maybe have spared my ship, regardless of what he said later, about never planning to spare the Enterprise? Or if I had run to another Federation area, instead of Earth? How many lives on Earth would have been spared, if I had just taken the ship to a starbase instead of Earth? Was trying to save Khan and make sure he faced true and fair justice worth the thousands of innocent lives lost in San Fransisco?". Kirk would likely have had to face these questions, and to explain his reasons for releasing Khan to grieving families who lost family members in those skyscrapers... definitely not a victory for the Enterprise crew, except they did arguably prevent a war with the Klingons ... for now ... but a victory for the Enterprise ... no, I'd say ...