Complex sentence: The Church accepted this separation from the state without qualms, as it wished to gain more independence, and considering that the head of state was the Orthodox Russian Emperor, complete integration with the state had been problematic for the Church.
Split into simpler sentences: The church accepted the separation from the state without qualms, as it wished to get more independence. As the head of state was the Orthodox Russian Emperor, complete integration with the state had been by no means unproblematic for the church.