Most of the major Pauline Epistles are mid first century, there were theological controversies as Christianity expanded but it's for sure not a state religion. It took centuries for the faith to dominate the pagan empire and the two got along pretty well well into late antiquity. Ultimately, many of the debates within Christianity in the fourth and fifth centuries are so obscure we can hardly understand them from a modern perspective- like the miaphysite controversy and countless others.
The other controversial issue from the council of Nicaea was the nature of the trinity. Many a holy war was fought over this exact issue for hundreds of years.
I understand what you are saying about Paul - but his assignment was to define a jewish sect for gentiles. That is what the epistles were. Paul redefined our modern understanding of Christianity by aligning the gospels with the intellectual class of the Roman empire.
When Constantine made christianity the religion of Rome he discovered that christianity was not well defined. Constantine created the Council of Nicaea to clean up the religion. It was a capitol offense to even believe some of the previous christian beliefs if the Nicaean council deleted your belief. Many many christians were executed.
Constantine then decided to make many Roman regions christian in name only. This included incorporating pagan gods as christian saints and adopting pagan festivals and other practices. Only a tiny educated class was expected to understand christianity at all. The uneducated class was not well regarded so that was OK.
The inquisition came much later. The intent of the Inquisition was to expunge the pagan adoption that started under Constantine. Most of the people executed during the inquisition were affiliated with pagan practices. Many of the women were pagan priestesses. At that time you had to read Latin to even understand the bible so I am sure the inquisition was confusing for most people.