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Modern historians have long known that the popular view of the Inquisition is a myth. The Inquisition was actually an attempt by the Catholic Church to stop unjust executions.
Heresy was a capital offense against the state. Rulers of the state, whose authority was believed to come from God, had no patience for heretics. Neither did common people, who saw heretics as dangerous outsiders who would bring down divine wrath.
When someone was accused of heresy in the early Middle Ages, they were brought to the local lord for judgment, just as if they had stolen a pig. It was not easy to discern whether the accused was really a heretic. The lord needed some basic theological training, very few did. The sad result is that uncounted thousands across Europe were executed by secular authorities without fair trials or a competent judge of the crime.
The Catholic Church's response to this problem was the Inquisition, an attempt to provide fair trials for accused heretics using laws of evidence and presided over by knowledgeable judges.
From the perspective of secular authorities, heretics were traitors to God and the king and therefore deserved death. From the perspective of the Church, however, heretics were lost sheep who had strayed from the flock. As shepherds, the pope and bishops had a duty to bring them back into the fold, just as the Good Shepherd had commanded them. So, while medieval secular leaders were trying to safeguard their kingdoms, the Church was trying to save souls. The Inquisition provided a means for heretics to escape death and return to the community.
Most people tried for heresy by the Inquisition were either acquitted or had their sentences suspended. Those found guilty of grave error were allowed to confess their sin, do penance, and be restored to the Body of Christ. The underlying assumption of the Inquisition was that, like lost sheep, heretics had simply strayed.
If, however, an inquisitor determined that a particular sheep had purposely left the flock, there was nothing more that could be done. Unrepentant or obstinate heretics were excommunicated and given over to secular authorities. Despite popular myth, the Inquisition did not burn heretics. It was the secular authorities that held heresy to be a capital offense, not the Church. The simple fact is that the medieval Inquisition saved uncounted thousands of innocent (and even not-so-innocent) people who would otherwise have been roasted by secular lords or mob rule.
Where did this myth come from? After 1530, the Inquisition began to turn its attention to the new heresy of Lutheranism. It was the Protestant Reformation and the rivalries it spawned that would give birth to the myth. Innumerable books and pamphlets poured from the printing presses of Protestant countries at war with Spain accusing the Spanish Inquisition of inhuman depravity and horrible atrocities in the New World.
For more information, see:
The Real Inquisition, By Thomas F. Madden, National Review (2004) http://www.nationalreview.com/comment/madden200406181026.asp
Inquisition by Edward Peters (1988)
The Spanish Inquisition by Henry Kamen (1997)
The Spanish Inquisition: Fact Versus Fiction, By Marvin R. O'Connell (1996): http://www.catholiceducation.org/articles/history/world/wh0026.html
With love in Christ.
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Did the eastern orthodox churches ever practice persectution of heretics?
We have kept our ordinances as it was at the very beginning and Orthodoxy has never changed its items, temples, rituals, it is living history. 
