I'm happy to see civilians running around in Modern Warfare 2's latest trailer, as well as fighters in civilian clothes.
I can only guess the scenes with people running away are during battles and not between. If there are civilians present during battles, with actual risk of civilian casualties, I consider that a big leap forward for first-person war games. War is never just between soldiers.
I have played games before in which it was possible to shoot the wrong people and be punished for it. Anyone who has played the Call of Duty games has been forced to restart from a checkpoint after shooting an ally. I believe that's the wrong way to punish such mistakes.
A reset means the offending action never happened. It's like a deleted scene or an expunged record. For mistakes to truly matter, they must remain part of the player's journey, an irrevocable moment which demands reflection and penance. If that moment can be erased, even in a punishment like a reset, then the player is not made to face it and reflect.
Civilians are important to war simulations (as opposed to arcade shooters) because they epitomize the moral complexity and uncertainty of war. Some civilians are hostile but not threatening. Some are dangerous in their foolhardy support. Some who would run away and seem harmless are dangerous, not by will, but due to the information they possess that enemies could gain by interrogation.
Fun over simulation -- I understand. But such complications of real warfare can make settings and stories infinitely more compelling, and potentially add replayability. Civilians are not a vital element for war games, but represent enormous untapped potential.