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.