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The snap code below has been tested only on D7. In case this code does not work on D6, check out the comments on this post here.

function MYMODULE_views_pre_view(&$view, &$display_id, &$args) {
  if ($view->name == 'VIEW_NAME' && $display_id == 'DISPLAY_ID') {

    // To find out the DISPLAY_NAME, FIELD_NAME and FIELD_VALUE use the devel module function
    // below to print them out.
    // Replacing 'footer' by 'header' works the same way.
    dpm($view->display_handler->options['footer']['DISPLAY_NAME']['FIELD_NAME']);

    $view->set_item_option($display_id, 'footer', 'DISPLAY_NAME', 'FIELD_NAME', 'FIELD_VALUE');

    // In this case scenario you needed to unset the footer display.
    // For the embedded view display you do like this:
    $view->set_item_option($display_id, 'footer', 'DISPLAY_NAME', 'view_to_insert', '');
    // For the normal text area display you do like this:
    $view->set_item_option($display_id, 'footer', 'DISPLAY_NAME', 'content', '');
  }
}