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Schaff, Philip. (2014). "Chapter III.Alliance of Church and State and Its Influence on Public Morals and Religion." In History of the Christian Church. (The Complete Eight Volumes in One). Volume 3, Nicene and Post-Nicene Christianity A.D. 311-600, from Constantine the Great to Gregory the Great. (pp. 1856-1908). (Original work published 1889). Amazon Kindle Edition. (Personal Library).
"§26. The Emperor-Papacy and the Hierarchy." (pp. 1895-1899).
Schaff observes that while Constantine was the first Roman emperor to claim oversight over Christianity due to his position as emperor, it developed significantly over the years, so that by the time of Justinian there was an imperial papacy (Schaff 2014, p. 1894). The view which developed was that of the bishops of the church dealing with its internal affairs, but the emperor served as a de-facto bishop dealing with external affairs. The seeds of this can be seen in the council of Nicea and in the fact that Constantine delivered occasional sermons to people, however did not involve himself in the controversy with the Donatists (Schaff 2014, p. 1895).
Schaff considers this difficulty of having spiritual authorities and secular authorities to be a situation which occurs to his time among Protestants. (Schaff 2014, p. 1896). The challenge is the interplay of internal and external affairs, or, if you will, spiritual versus temporal affairs. From the time of Constantine on, emperors and other rulers took part in councils, nominated or confirmed churchly leaders, and sometimes sided with orthodoxy and sometimes with heresy.
While Schaff considers the work of the Church to have restrained the despotism of the emperors, the imperial leadership was also able to move affairs of the Church toward their own ends (Schaff 2014, p. 1898). This was more true in the Byzantine court than in the Roman court. In the Byzantine court the imperial power "degenerated into an insufferable tyranny over conscience" (Schaff 2014, p. 1899). In Schaff's opinion this was very damaging to Christianity in the east.
"§27. Restriction of Religious Freedom, and Beginnings of Persecution of Heretics." (pp. 1899-1907).
One consequence of the alliance of church and state which Schaff finds particularly troubling was the role of the civil government to restrict religious freedom and to punish those who departed from the doctrinal standards of the church (Schaff 2014, p. 1899). It was simply more difficult for the church to deal with doctrinal matters than it had been prior to the Nicene period. Those who were in need of correction could be instructed and hopefully persuaded. Those who refused the needed correction were excommunicated. The imperial involvement added the difficult situation of excommunication leading to accusation of crimes agains the state (Schaff 2014, p. 1900). Civil penalties eventually included punishment by death.
Schaff finds that in terms of general reputation before the world, the confusion of churchly and civil authority and penal systems has been problematic. The negative impressions caused by Christianity's appearance as a governmental organization which does not tolerate pluralism is offensive to many in modern civilization (Schaff 2014, p. 1901). The distinction between churchly and civil authority has become more apparent since about the 18th century.
The background of the confusion of churchly and civil authority is rooted in Constantine's work. While he initially tolerated any religious group, he then began moving toward less tolerance for pagainsim. As that died out, intolerance was increasingly focused on those who were outside the bounds of orthodoxy, however the reigning emperor would define it (Schaff 2014, p. 1902). In effect, the emperors exercised their power to promote whatever view they wished, and they used their influence as the civil bishop to exercise that authority within the Church. Bishops of the church generally were more focused on matters of repentance and restoration, though they would certainly excommunicate heretics. However, many would speak out against imposing capital punishment on people due to heretical views (Schaff 2014, p. 1904). Schaff does note that both Jerome and Augustine eventually reached a conclusion that persecution against heretics could be appropriate due to the great danger of their persistent teaching (Schaff 2014, p. 1905).