You will need to find where in the theme that the theme loads its jQuery and remove the call. That is where I would start. Then cross your fingers.
I have some concerns though. Your theme is loading an older jQuery-- jQuery 1.4.2-- and it is loading a bunch of javascript of its own. If you use jQuery 1.4.2 you may have conflicts with your Colorbox plugin, or any number of newer/recently updated plugins. If you use jQuery 1.7.2, which is what WordPress is loading, you may have conflicts with the theme's scripts which were written for 1.4.2.