Initialize WordPress customizer variables

I believe that all you need to do is pass defaults to get_option

function init_theme_options() {
  // check to see if theme options are set
  // Not sure how your options are organized but...
  $defaults = array(
    'opt1' => 'stuff1',
    'opt2' => 'stuff2'
  )
  $theme_options = get_option('theme_option_name',$defaults);
}

If you want to see a very complicated version of this, look at how Twenty Eleven does it.