In regards to this story as a strong hint as to what Goyer's super-duper secret script has in store for Man of Steel, it seems we are looking at Superman being interpreted as a threat by the military, as part of the potential storyline.
Notice that in the Action Comics #900 story, there are Marine snipers with kryptonite rounds ready to take Superman out...even though Superman has been a hero for years....they don't completely trust him.
So this may point out that Superman's relationship with the U.S. government (or other governments for that matter) will likely be a tenuous one at best, similar to the one depicted by Goyer in this now famous story.
So those of you who were speculating that there is a similarity between the Incredible Hulk movie storyline and the new Man of Steel movie script (meaning it will be the U.S. Military vs. Superman), may be on to something, if Goyer's recent Action Comics story is any indicator of his general perspective how Superman should be.