Remove commerce item from cart
Orders have a removeItem method defined on their interface. You just need to pass the loaded order item to that method, and then delete the orderitem.

/**
 * Removes an order item.
 *
 * @param \Drupal\commerce_order\Entity\OrderItemInterface $order_item
 *   The order item.
 *
 * @return $this
 */
public function removeItem(OrderItemInterface $order_item);