Fact From the Vapor of Nuance
Marvel has put this alternate opening scene of The Avengers online for the viewing, as part of its ongoing campaign to get people psyched for the DVD release of the movie (which could have just been accomplished by officially releasing the blooper reel, I mean, come on), and it's totally understandable that this didn't make it into the final film. It places the film in an entirely different sort of narrative loop by beginning with the end, and more than that, it's completely at odds with the tone of the rest of the movie. The Avengers was big, bombastic, optimistic, and blissfully consequence free (aside from a certain S.H.I.E.L.D agent and his friends).
What this scene, chock full of Cobie Smulders, feels more like is the opening scene or the teaser trailer for The Avengers 2, a movie that plays up the tension between Smulders' Maria Hill and Samuel L. Jackson's Nick Fury, in the lead up to the colonel being removed from his command just when the world needs him most.