Fallout 3 allowed you to murder innocent people, wandering nomads, traders, basically anyone (well except kids), even a guy collapsed on the ground begging for water. In fact, any CRPG worth it's salt doesn't balk at the idea that not everyone is a noble minded hero and that innocent civillians are not impervious to all attacks.
Deus Ex allows you to kill innocent people, even sick people. Hell there is one small part where a guy asks you to kill him.
All of the Hitman games, Blood Money in particular, contain numerous civillians that you never ever have a reason to kill, yet the game provides no specific punishment for doing so.
Soldider of Fortune 1 and 2 would automatically kill you if you shot anyone but the bad guys. And it was a worse game for it.
Strife apparently had the vital signs of all civillians hooked up to the global alarm system and anyone that was killed would set it off, and they always knew it was you. Never did work out how they knew.
The Grand Theft Auto/Saint's Row games obviously have a police presence to attempt to stop you from killing too many people, which is accurate to the scenario and a entertaining facet to the game.
I'm sure there are more. I imagine that the majority of older games didn't have civillians because there was only so many system resources to go around and it was a waste to spend them on non-enemy, non-quest related, non-vendor characters
If anything, this Modern Warfare 2 outrage is another reminded for me to put on my "get off my lawn" t-shirt and pine for a time when gaming was a secluded pastime seperate from society and it's impressive ability to freak out at anything and everything.