This would require you to customize the js code in the php file that is included for the map. In here you should be able to see where the markers are being set, the color of the marker should be in the name of it.
You could add in a ternary type expression to make it choose one colors file over the other like this:
(($_rowYourRS['your binary column'] == 1)?color 1 file:color 2 file)