Why does it matter that they are treated as one screen other than the fact that the menu bar goes across both screens and the dock, if centered, would be split across both as well? (Okay, I know that you wouldn't be able to move around each individual screen in system preferences, but if you are just using those two screens side by side, who cares?)
EDIT: I wonder if there is a program that would allow you to move the dock off center but still on the bottom of the screen to get around the screen splitting program...
you can use onyX to align the dock to the left or the right instead of the center of the screen, but this does not guarantee that the dock will not be split between the screens. you can use a small dock icon size and magnification to make the dock stay on one half of the desktop.