I dearly wish there was some option to help control civilians. Seeing them running towards the alien instead of within the perimeter established by my agents is just painful. Some amount of "civilian stupidity" could work, like a chance to run towards another recently shot civilian ("Jenny!! NOOoooo!!!! *too late*) but their totally random behavior is annoying.
I never thought of stunning civilians to bring them to safety, but It could somewhat work if they woke up behind XCom lines where their life isn't at risk. Some kind of improvement could be made, even though it is well beyond my abilities...