You would have to loop through the cart to find the item you wanted to delete and then delete it... this function would do the trick:
function DeleteByID($cart,$id) {
for ($n=0; $n<sizeof($cart->Items); $n++) {
if ($cart->Items[$n]) {
if ($cart->Items[$n]->ID == $id) {
$cart->Items[$index] = null;
$cart->ReIndexContent();
$cart->ResetAll();
$cart->SaveCart();
}
}
}
}