If the church and state were two totally different entities how was it treason and punishable by death?
In the past, many secular governments considered it to be treason for anyone to be of a religion other then that of the ruler. This attitude dates back to pre-Roman and pre-Greek times. Aristotle wrote on the subject coming to concluding that it was treason. European secular governments tended to agree with this.
In the 1100’s several European secular governments reinstated laws making it treason for a Catholic to commit heresy to be a non-Catholic since they were Catholics… not members of the Catholic clergy, just Catholics. At that time of history, it was actually considered to be forward thinking to allow other religions to exist in the kingdoms. But the rulers demanded obedience from their Catholic subjects, which included not committing heresies. It is the concept of declaring an official state government… this is of course outlawed in our constitution.
These governments started to declare people heretics and punishing them mostly through death. They had no court system, no protects for the accused. Their conviction and execution rates were high. Further, the popular opinion was that people hated heretics. It was not unusual for a crowed to declare someone a heretic and kill them on the spot. One of the early cases was of a Bishop who burned the cross in protest. He was arrested by the secular authorities with no involvement of the Church what so ever. The town’s population was so angered at him burning the cross that a crowd broke into the jail, hauled him out and burned him alive… they felt that was a fitting end for someone who burned the cross. These types of things where gangs took the law into their own hands when it came to heretics were common in those days.
So the Church stepped in and told the secular governments and local people that only the Church had the authority to determine who was a heretic. They feared, rightfully so, that the secular government would loosely accuse anyone they wanted to get rid of as a heretic. This is why the inquisitions started on a more organized scale then they had ever been before.
Contrary to myths and actual outright distortions told by anti-Catholics, the inquisitions were court systems light years above the state of civil authority at the time. Most civil authorities did not have courts of any kind. The did not allow anyone a defense.
The Church put in place a system that is the pre-cursor for the court system we follow today. A person had to be accused by 2 or more people for the Inquisition to even take it seriously. The accuser was told of their charges and provided with the evidence. They had 3 months to reply to the charges and could hire an attorney to represent them. The final decision was made by a jury… not by the inquisitioner. The inquisitioner was more like what we call a prosecutor today. To protect the witnesses their identities were not divulged. To protect the accused their identity was not divulged to the jury either. The juries were typically made up of 20 to 45 people… lawyers, local leaders, etc… people who were respected in the community. Once a verdict was handed down, the accused could appeal their case to a higher court.