on the confirm page, add an if statement around the form tag that sends the transaction to paypal so it will only go to paypal if the cart grand total is greater than 0:
<?php if($eCart1->GrandTotal() > 0) { ?>
<form name="checkout_PP_LI_Hid" action="https://www.PayPal.com/cgi-bin/webscr" method="post">
<?php } else { ?>
<form name="checkout_PP_LI_Hid" action="checkout_success.php" method="post">
<?php } ?>