Modify Javascript Configuration Options for Theme Customizer Colour Picker

The color picker thing is registered as a jQuery UI widget, so you could modify its prototype object before the widget is used in the page:

add_action('customize_controls_print_footer_scripts', function(){

  ?>
  <script>

    jQuery(document).ready(function($){

      $.wp.wpColorPicker.prototype.options = {

        border: false,
        // other options here...

      };         
    });   

  </script>
  <?php

}); 

(You should put that in your .js file)