Changing the resolution is done with a separate program (CoCDCoTELauncher.exe under \engine\) before launching the game.
To make 4:3 resolutions maintain aspect ratio on a widescreen monitor, you have to set your graphics card to scale the image to Aspect Ratio on the GPU (not on the Display, which is the default setting). This would be under the NVIDIA control panel - > Adjust desktop size and position if you're using an NVIDIA card.
I highly recommend playing the game at the correct aspect ratio for whichever resolution you end up using because the field of view and visual design of the game is nauseating if the image is stretched, more so than many other first person games it seems to me. Lots of muddled, dark desaturated low poly environments and character models and forced camera movements and field of view changes during play.