As a professional historian, I can tell you as a fact that “millions” did not die as a result of the Inquisition. Firstly, the Inquisition never even came to the New World. There was no point to it, since Native Americans were not heretics. In fact, they were given a protected position by many laws enacted by Spain and Portugal. Now… millions DID die as a result of exploitation by the Spanish and Portuguese, who used them as slaves, or who were exposed to new diseases they had no immunity to, but this was ILLEGAL under Spanish law, and this was a SECULAR exploitation that was condemned in the strongest possible terms by the church. However, due to the distance, many of these protective laws could not be enforced. (A good book to read about the topic would be “Bartolome de las Casas” by Lawrence Clayton.) Also, since Brazil, Argentina, etc. were colonies of Spain and Portugal, Protestants were forbidden from moving to the area. Aside from a few pirates, you don’t see any Protestants in these countries until the mid 1800s.
Now, in Europe, modern historians have made a thorough attempt to reconstruct the trials of the Inquisition. This is not as hard as it sounds, since the Inquisition actually kept excellent records. Interestingly, many people (especially in Spain), given the choice between being tried by the secular government or the church, actually chose the Inquisition, because the Inquisition, despite the problematic practices of torture and burning at the stake, actually made a reasonable effort to determine someone’s guilt. The secular institutions of the time were somewhat more lax and corrupt. Second, figures show that less than 1% of all of those who went on trial were actually executed. Believe it or not, the most common ruling in an Inquisition trial was “not guilty”. Among those that were found guilty, fines and penances were often the penalty. Although the exact number is a matter of some debate, it appears that no more than about 20,000 to 30,000 were executed in the entirety of the Inquisition across Europe. In Spain, the average number of executions works out to less than just 125 per year.