Go into System -> Preferences -> Keyboard
Click on the "Layouts" tab and then click the "Layout Options" button.
Click on "Alt/Win key behavior"
Select "Control is mapped to Win keys (and the usual ctrl key).
This will make your Apple command keys act like control, and keep your ctrl key as control as well. However, this will leave you without a Super key. I haven't found this a problem. I hope that's what you're looking for!