Fetch user's realname (from Name Field) within database query (or an alternative method)?
The Name project used entity fields that can be queried in the DB, just like any other field. All you need to know is the machine name of field that you attached to the user entity. To use your example above:

$result = db_query("
    SELECT 
        field_data_field_user.field_user_target_id, 
        nf.*,
        users.name
    FROM field_data_field_user
        JOIN users
            ON field_data_field_user.field_user_target_id=users.uid
        JOIN field_data_field_MY_NAME_FIELD AS nf
            ON nf.entity_id=users.uid AND nf.entity_type = 'user' AND nf.bundle = 'user'
    WHERE field_data_field_user.entity_id = :nid", $args);


All you need to do is replace MY_NAME_FIELD with the machine name of your actual field.  The result will be rows that contain name columns associated with the user reference.