カウントの結果を条件に含める
HAVINGでおk
SELECT customer.*, COUNT(customer_user.id__customer) AS COUNT__customer_user FROM customer LEFT JOIN customer_user ON customer.id = customer_user.id__customer GROUP BY customer.id HAVING 0 < COUNT__customer_user
SELECT customer.*, COUNT(customer_user.id__customer) AS COUNT__customer_user FROM customer LEFT JOIN customer_user ON customer.id = customer_user.id__customer GROUP BY customer.id HAVING 0 < COUNT__customer_user