How to tell variable_get to get the value from the database and not the $conf array?
I don't think Drupal core has anything like that, no. For speed and efficiency, the variables array is in memory pretty much as soon as settings.php has been processed.

You've always got db_query():

$var = db_query('SELECT value FROM {variable} WHERE name = :name', array(':name' =&gt; 'var_name'))-&gt;fetchField();
$var = unserialize($var);


It would be trivial to build up an efficient variable_get_from_db function based on that.