"I will tell you what you did with Atheists for about 1500 years. You outlawed them from the universities, or any teaching careers, besmirched their reputations, banned or burned their books or their writings of any kind, drove them into exile, humiliated them, seized their properties, arrested them for blasphemy. You dehumanized them with beatings and exquisite torture, gouged out their eyes, slit their tongues, stretched, crushed or broke their limbs, tore off their breasts if they were women, crushed their scrotums if they were men, imprisoned them, stabbed them, disemboweled them, hung them, burnt them alive. And you have nerve enough to complain to me that I laugh at you"
Dr. Madalyn Murray O Hair
Very hyperbolic, but the general point is well taken.
The statement isn't meant to give an all-encompassing summary though: she's directly affirming that all of this happened for 1500 years, and she also seems to be implying that any individual atheist was bound to experience many of the punishments.
That's clearly hyperbolical.
As for the Inquisition (and the Middle Ages generally), most of the torture methods mentioned above would have never been used there. The Medieval Inquisition thought spilling blood was a sin, for instance: that's why a version of water-boarding was their preferred torture method. Ironically, the same torture method used by the Bush administration.
Most of the torture methods ascribed to the Middle Ages (which is when the Inquisition was active, largely) are pure fantasy anyway. They say more about the lurid imaginations of the Victorian historians villifying the Middle Ages than anything else.
The Victorians really did screw up the way in which we look at history didn't they?
Richard the Lionheart became a national hero in England for instance as a warrior for (imperialist) country and god. In reality he was a French noble who hated England and the English and caused massive financial issues for the kingdom.
I guess that people need symbols to motivate them, too bad that the inquisition is so often used as a symbol for what's wrong with the church (or religion in general) which usually includes exaggerations or straight up lies.