I don't think this will happen.
If it did though, the military would love the opportunity to test it's non-lethal equipment. Heat rays, rubber pellet grenades & claymores, sticky foam, and enough tear gas to blot out the sun. Heck even jet engines blasting up a sandstorm would work. I also can see the military jamming GPS and communications in the area too, just so the Naruto runners can't congregate and co-ordinate.
Of course this being Area 51, they could have an industrial sized neuralizer a la Men in Black.
Spectating this would be cool.