Violence is the question. The answer is always "yes."

Most games require you to face enemies to advance the plot, and give you a set of tools to do this with. Most of the tools are weapons, only on rare occasions stunners or tranquilizers. Few games give you a non-violent alternative, and those that do seldom give you any reason to use these alternatives. Even those with non-lethal options tend to give the more permanent solutions a leg up by having ko'd opponents recover after a short time.

Scenario:
You are Sergeant Awesome, on a mission to rescue Senator Kidnapped from a terrorist group that needs him to provide codes for some nuclear-biological-giant robots powered by the sheer improbability of their existence or something. It's probably not too important. You come across a small group of terrorists away from the main force. Sneakily, you sneak up on their leader and hurl him off a cliff. Little did you know:



And now the men he was preparing to lead against their leader are attacking you, and others are rushing up from places unseen. Maybe, just maybe you could have joined them, weakening the resolve and ability of enemy forces.

The MGS series is far better about this than most games, theoretically allowing you to complete the game without killing a single enemy or even being detected. Better still, in Portable Ops you could recruit enemy soldiers by knocking them out and dragging them back to your base. And to hammer the point home, your ranking at the end is influenced by how many times you were seen and how many enemies you killed. Hell, in MGS3 there is a level forcing you to revisit every person you have killed in the game, making it beneficial for you to not kill wherever possible.

Even so, knocking out enemies is still violence. The games where you can deal with enemies in any non-violent manner aside from running away are few and far between and, while I love me some shooties, I think we can do better. An excellent example is Portal, and that was an almost universally loved game. It proved that it is possible to have a game where you don't kill anything, don't even hurt anything (almost), be just as entertaining and compelling as any FPS. This was promptly ignored. Still, it's an increasingly uncommon thing.

It's not that violence is morally apprehensible or wrong, but rather that it's limiting. Designers and audiences and the industry as a whole are attached to the idea of an adversary, an opponent who must be overcome. This weakens video games in general, limiting us to problems that can be solved with dakka and boom, giving us heroes more about destruction than salvation, and shallowing the pool of ideas until we are left with gray and brown space marines defending humanity again.