The function needs to be altered a little bit for anyone else looking to do the same thing. Only change was to remove ORDER BY in the new SQL statement.
add_filter( 'posts_clauses', 'mb_sort', 99, 2 );
/**
* Sort just the POST relationship by date DESC.
*
* @param array $clauses Existing clauses.
* @param WP_Query $query Main Query.
* @return array
*/
function mb_sort( $clauses, $query ) {
$relationship = $query->get( 'relationship' );
if ( ! $relationship || 'REL_ID' !== $relationship['id'] ) {
return $clauses;
}
$clauses['orderby'] = 'post_date DESC';
return $clauses;
}