I can't recall exactly for NVidia, but I know for ATI you look in the Video card control panel for a scaling option and set it to maintain aspect ratio or use centered timings. Perhaps for NVidia it is similar.
I do believe NVidia is similar, however they seemed to have dropped this option from a certain forceware version on. I do not have this option in my NVidia control panel on my 8800 GT, I might be able to install older drivers and gain this option, however I'm not sure if it will make a difference due to the fact that I can set my monitor to do the same thing, but I will give it a try.
I had another idea as well, I was thinking of using VMplayer to create a windows XP virtual machine, install the game and run it on that. In theory I would have an entire Virtual Machine running in a window, and thus could get the 4:3 aspect ratio, it will just take some time to install XP on the virtual machine, run windows update, etc...
I learned the hard way that you cannot use aspect ratio scaling unless the Nvidia Control Panel detects you monitor as an LCD, which it doesn't if you use a VGA cable. I had to buy a DVI cable before I could set the aspect ratio. maybe you have the same problem.
The 8800 GT doesn't have VGA, only DVI. I use an HDMI cable from my monitor to DVI converter at the video card. I have read that Nvidia dropped the aspect ratio scaling option from certain cards/drivers but I'm not sure. MY monitor handles this perfrectly though for pretty much everything I wanted to put in 4:3 until this game. For some reason this game overrides my monitor's settings, which is very odd. I keep thinking there has to be something simple.
I checked the config file but there is nothing that I can see that would be of use. There was an option to stop the cinematic (movies) from stretching but not the actual game.