In the evolution of man instinct came to play a vital role since Nature fine-tuned his physiology to address the question: flee or fight? The adrenalin rush of your body in sensing danger is of different make up than when you need to think seriously what is the best course for your future. In the latter case time is on your side and you may weigh pros and cons to arrive at a conclusion. This is what thinking means. You brain is not merely reptelian brain but has also complex rewiring to help you in the process. Speech, visual and other faculties are controlled from locations that can be mapped and studied. Thus nature has provided certain initial back-up to which your life among men and animals add ancillary support. The thinking machine Head has its adjunct the Heart with which your feelings reinforce your life experience. Basic emotions fear and pleasure have myriad shades of meaning to make your life significant. This is what makes man different from animals.
Such a man also has rational and irrational side to which I only need to point the wakeful state and the dream state. If you go by the latter irrational side alone you are a menace to the society and you might require supervision and medicine to keep you from harm. The point is the head should remain in its place and consequently the heart must hold its own. The relationship of State and religion is like this.
In order to understand how poorly religion and state can hold together we only need to look at the Church of Rome.
In the Early Church the bishops elected for the office were considered as shepherds of the flock. Following the stricture of Jesus to Simon Peter they were to cater to the spiritual needs of the early converts who were mostly marginalized in society or were actively hounded out by Rome as a threat to the empire. As seized of their charge the early bishops did not dabble in temporal matters. The serious threat to the religion actually came from the time Constantine made Christianity as the state religion. He made it not out of any genuine conviction but as a matter of state policy. Such explosive mixture could only delay but not prevent the march of events. The empire was doomed to collapse and it did happen. With it the primary aim of the Church was seriously compromised.
After the fall of Rome during the “Middle Ages”, the papacy was influenced by the temporal rulers of and surrounding the Italian Peninsula; these periods are known as the Ostrogothic Papacy, Byzantine Papacy, and Frankish Papacy. Over time, the papacy consolidated its territorial claims to a portion of the peninsula known as the Papal States. Thereafter, the role of neighboring sovereigns was replaced by powerful Roman families of which I may merely mention the Tusculan Papacy.
From 1048 to 1257, the papacy experienced increasing conflict with the leaders and churches of the Holy Roman Empire and the Byzantine Empire. The latter culminated in the East-West Schism, dividing the Catholic Church and Eastern Orthodox Church. While Popes were politicking the Church underwent through serious spiritual crisis among believers that came in the form of the Black Death. With such a calamity for the suffering flock the Church failed to address their spiritual confusion. They believed it was the divine chastisement and came from God. ( The Black Death wiped out nearly two thirds of Europe and the Pope sat out through this terrible times in Avignion,France. No wonder the survivors came out with a new idea of making their present life count. The Carpe Diem effect. This led to Reformation and the Enlightenment in course of time. Initiative in trade and commerce had passed from Italy to Germany, England and Holland.)
The Church was split by politics rather than any theological disagreement that quickly escalated from a church problem to a diplomatic crisis that divided Europe. Secular leaders had to choose which claimant they would recognize that showed the lie that the authority of the Pope came straight from St. Peter. The schism was ended by the Council of Constance (1414–1418).
Islam also suffers from the same tragedy. Petro-Islam is out and out buying converts who fit neither here nor there. Their head is a counting machine while their heart is far from obedience to their God.
P.S: The tragedy of putting the cart before the horse , mistaking the heart for the head led to the decline of the Church and Italy never survived the Black Death. In a manner of speaking the medieval mindset still plagues them. Unification of Italy was hampered by Papacy and the present economic crisis owe partly to it. We see conjugation principle at work here.