We have seen systems like that before. The Confucian Bureaucracy that went against the will of many Emperors. The Meiji system in Japan where the Army and Navy had power over the Emperor, the Diet and the Prime Minister. The old Soviet system where the power flowed from the Politburo and the various Soviet Ministries, not the Central Committee as intended. even the old Russian Imperial system where the nobles as a class controlled the government Bureaucracy.
All of those systems had bad endings, in the case of the Chinese system, multiple times as Dynasties were overtaken by outsiders after becoming stagnant.