http://pradeepsanku.com/tag/delete-product-from-cart-in-magento-programmatically/
<?php
$id = '100'; // replace product id with your id
$cartHelper = Mage::helper('checkout/cart');
$items = $cartHelper->getCart()->getItems();
foreach($items as $item):
if($item->getProduct()->getId() == $id):
$itemId = $item->getItemId();
$cartHelper->getCart()->removeItem($itemId)->save();
break;
endif;
endforeach;
?>