religionnews.com uses the Zoninator plugin to control our front page story hierarchy. This function collects our 'Headlines' zone as part of the main front page query, rather than ignoring the main query and starting a new one.

wp-zoninator-main-query.php

add_action( 'pre_get_posts', 'rns_get_headlines_zone', 10 );
/**
 * Get the posts in the 'Headlines' zone in the front page main query
 *
 * @param obj $query The query to pass to the database
 * @see Zoninator's get_zone_query()
 */
function rns_get_headlines_zone( $query ) {
  if ( ! is_admin() && $query->is_main_query() && $query->is_home() ) {
    global $zoninator;
    $query->set( 'order', 'ASC' );
    $query->set( 'posts_per_page', -1 );
    $query->set( 'post_type', $zoninator->get_supported_post_types() );
    $query->set( 'ignore_sticky_posts', '1' );
    $query->set( 'post_status', 'publish' );
    $query->set( 'orderby', 'meta_value_num' );
    $query->set( 'meta_key', $zoninator->get_zone_meta_key( 'headlines' ) );
  }
}