As demonstrated on September 11, 1857 at Mountain Meadows, Utah?
While I am loathe to defend many aspects of the Roman church, your figures are most certainly inflated, though not unexpected when defending a cult. The details that I am able to locate show a figure of 5-6,000 over several centuries, with perhaps half of those being Protestant. The rest were Jews and Muslims who publicly converted to the Roman faith, but kept their old faith practices while in private.
FWIW, there was some mercy and order involved in the inquisitions. Only 2% of the trials resulted in execution. The MMM? 100% of all but small children were murdered. During the trials, the Roman church officials wore their religious garb and those on trial, knew they were on trial before a court of some kind. The MMM? Trial? What trial? The Baker-Fancher wagon train was attacked by cultists, dressed as Natives then, the victims were summarily shot by more cultists. The Mormon church then tried to cover up the masacre and blame it on the Indians.
Another difference: The Roman church owns up to their action. The Mormon cult? No.
About 12,000 ... but they actually got trials and got to speak in their own defense, instead of just being murdered in cold blood, like the people at Mountain Meadows. And they were all Catholics, or claimed to be, unlike the victims at Mountain Meadows, who were killed because they weren't Mormons.
So you're really comparing apples to oranges.