If we did learn that U.S. governmental agencies were using science and sorcery to make super-soldiers for wet-work, would any of us really be surprised? Does anyone think that something along the lines of Treadstone or Blackbriar doesn't currently go on?
What happens as the film goes on in is best left for viewing by Bourne aficionados. The script is thin, but the acting, cinematography and direction make up for this loss. This is worth seeing even by the naysayers.
The Avengers doesn't solve this problem of what to confront for us. Art rarely gives us definitive answers; it more often asks questions than answers them. But by bringing this current to the service, it could at least remind us of the possibilities open to us.