Remember Dan Goyer, who wrote the screenplay for MOS, also wrote the citizenship story in Action #900. In that now notorious tale, we get a glimpse of how the U.S. government/military deals with a Superman that the world has embraced as a hero for many years. And how do they do that? When Superman is speaking to a government official, there are U.S. military snipers with Kryptonite bullets, hiding in the bushes, intent on taking him down if the need arises.
If this is how Goyer interprets the relationship between a Superman, that has been active for many years, and the U.S. government, that has known about interacted with him for all that time, then it is clear that by the end of the film, the new Superman will likely still be a vigilante. The people of the world may all love him by the end of the movie, but governments can't.
Remember, even if the U.S. gov were to trust Superman and know him to be a good fellow, it would be totally irresponsible of them to not develop the means to take him out in case one day he were to go rogue, be controlled by another being, or switch allegiances.
And after having to deal with (or at least witness the fury of) Zod and Faora, there is no doubt the military will see Superman as a high potential threat, no matter how much good he does.
I guess that will be the new status quo in the comics as well.