You need to add a meta query, which will specifically select those posts that have both the meta key you want, and the desired value.
$args = array(
'post_type' => 'pages',
'order' => 'ASC',
'meta_query' => array(
array(
'key' => 'use-this-page-as-a-section', // or whatever the key is
'value' => 'yes'
)
);