You could make a general "config.php" in each site's web space, and add site-specific configurations like so:
<?php
ini_set('sendmail_from', 'noreply@site1.com');
?>
Then, you would simply include the appropraite config.php in each script.
Alternatively, you could simply set this address each time you send mail:
ini_set('sendmail_from', 'noreply@site1.com');
mail($to, $subject, $message);
EDIT: Setting the addresses in the custom headers, as mentioned above, is probably easier yet (just make sure to change that semicolon after Reply-To to a colon 😉).