Just some thoughts, many of the priests, teachers of theology and the high priest during Jesus' time thought Jesus was a heretic. It was the established church that put Jesus to death, even the pagan Pilate said "I find no fault in Him". The very individual that was sent to save them, they crucified and closed the door of their own salvation.
If there was ever anyone who qualified as being heretics, it was those who were determined to put Jesus to death. But what was Jesus response? Stone them? Burn them at the stake? No, instead He prays on the cross "Father forgive them".
In the book of Acts it is again those who claim to be following God who are trying to put Paul and the other apostles to death. They thought they were following God and would receive rewards for their zeal, but in the end they will be greatly disappointed.
During the dark ages the Bible was chained to pulpits and limited access was granted only to priests and theological leaders/scholars. This suppress of the scriptures resulted in theological and spiritual straying away from the teachings of Christ for we have this divine promise,
"Cease listening to instruction, my son, And you will stray from the
words of knowledge." (Proverbs 19:27)
The Lord raised up a handful of faithful men who began to translate the Scriptures into the common languages and distribute them to the masses. This would result in a fantastic revival for the word of God has power to revive the soul for it is written
"It is the spirit who gives life, the flesh profitteth nothing, these
words that I speak to you, they are spirit and they are life". (John
When man began to regain knowledge of the word of God, they learned that just like in Jesus' time, men had made merchandise of the grace of God. Like those selling in the temple courts whom Jesus declared "Take these things hence; make not my Father's house an house of merchandise." (John 2:16) now men were claiming the forgiveness of sins by simply paying money to the church. The infinite sacrifice of Christ was lost sight of. When Simon the sorcerer tried to purchase the gift of God with money, the apostle Peter declared
“Your money perish with you, because you thought that the gift of God
could be purchased with money! You have neither part nor portion in
this matter, for your heart is not right in the sight of God. Repent
therefore of this your wickedness, and pray God if perhaps the thought
of your heart may be forgiven you. For I see that you are poisoned by
bitterness and bound by iniquity." (Acts 8:20-23)
Men began to protest against the abuses of the Church and a reformation began. Those who rejected the light of God's word followed the same path as the scribes and Pharisees of Jesus' time. They began to persecute unto death. This was no surprise for it is written
That which has been is what will be, That which is done is what will
be done, And there is nothing new under the sun. (Ecclesiastes 1:9)
A good history of the inquisition can be found here - http://www.whiteestate.org/books/gc/gc.asp