I'm not sure I would agree with the term "fair". I would imagine that the Inquisition was just as tough as the people on the other side. It was just a completely different world then.
How one gauge how many people died during this era would be meaningless. Some people wanted to die rather than recant. Although not part of the Inquisition, Sir Thomas More was more than happy to die for the Church simply for telling King Henry not to fool around. Catholics were putting Protestants to death while Protestants were doing the same. Martin Luther, had to go into hiding after he refuse to recant because Catholics wanted to kill him. The Pilgrims came to this land to get away from religious persecution. I think the Inquisition is only a small piece of a larger picture.
In a way it was a different world in which people put a very high value on religion which was often mixed with politics. It's difficult to judge anyone or to ever know how many were killed (what about the War of the Roses) on religious beliefs. However, one has to wonder if we haven't become too complacent not wishing to offend anyone and trying to whitewash history where our forefathers were willing to die for their cause. Are we that ashamed?
The point here is that credible research shows that the Inquisition was painted all black in the past, not that it needs to be whitewashed.