I agree with you on this one. The Catholic church almost certainly killed more, but the numbers are close enough.
While I would say that far too many have died at the hands of those who claimed to have the interests of Christianity at heart, there is little verifiable information availiable to suggest that the Protestant community was in any way better than the Catholic, although there are abundant claims to the contrary. As a rule of thumb, though, Europe has always been better at being Barbarous than the Romans. (something to keep in mind),
"Contrary to widespread belief in the nineteenth and early twentieth centuries, the Inquisitors were, with few exceptions, not psychotic sadists who were insatiably seeking vengeance upon heretics through death penalties. The Inquisitors were normally well trained canon lawyers and frequently Dominican friars or members of another religious order.RECENT RESEARCH HAS SHOWN THAT THEY WERE SUFFICIENTLY ASTUTE TO BE SKEPTICAL OF THE WITCHCRAFT CRAZE OF THE FIFTEENTH AND SIXTEENTH CENTURIES AND TO FIND THE VAST MAJORITY OF THE ACCUSATIONS AGAINST OLD WOMEN AND SIMILAR MARGINAL PEOPLE WHO WERE ALLEGED TO BE WITCHES TO BE WITHOUT SUBSTANCE.
Therefore, the courts of the papal mandated Inquisition should never be considered in the same category as the Nazi holocaust or Stalinist purges. Surviving Inquisitorial records are sparse. But it is a good guess that even including the Spanish Inquisition of the late fifteenth and sixteenth centuries, which in a more Draconian fashion operated directly under the aegis of the Spanish crown rather than the papacy,
THE TOTAL NUMBER OF PEOPLE WHO DIED AT THE HANDS OF THE CATHOLIC INQUISITIONS DID NOT EXCEED FIVE FIGURES AND PROBABLY DID NOT TOTAL MORE THAN TEN THOUSAND PEOPLE." [over hundreds of years]
N. F. CantorThe Civilization of the Middle Ages. Harper: New York 1994
The Protestant "Inquisitors" were much less astute and they did mostly burn old women and other marginal people. The Roman Inquisition was executing a few tens of people a year, while in Germany thousands of innocent women were burned at the stake by Protestant (mostly) fanatics. The difference was that the men burned by the roman Inquisition are very famous, like Giordano Bruno, while the women burned in Germany are largely nameless.