Goa Inquisition

I'd say the record speaks for itself. 500 Spaniards leading Armies of Moctezuma's former subject peoples against Tenochtitlan. Armies that numbered in the tens of thousands. My impression is that you are really drawing a parallel between the Spanish conquest of Mexico and Muslim conquests of parts of India. I cannot really reply to the second, and I don't believe you've really studied the first. The Inquisition in Spain was used primarily as an instrument of state, to weld Spain into a single nation. As such, its methods and goals would have differed from the Inquisition in Portugal. The exception to this would have been the period in which Spain essentially annexed Portugal, a la the 1938 German takeover of Austrian via the "Anschluss". When Portugal was not under Spanish domination, it was not a part of the Holy Roman Empire as it was under Carlos V and Filipe II. I'll take your word as to how it was applied in India during those times, but to place the Inquisition in context, it is necessary to also look at the state of religious tolerance outside the Catholic areas. Remember that the Salem Witch trials took place among a sect of Protestant reformists, and even the recent Chiapas rebellion in Mexico had a certain religious tinge to it that reminded this reader at least of Europe in the 1500s.

In summary, there was no 'genocide' in Mexico unless we are willing to dilute that term to the point it loses all meaning. One civilization replaced another. The peoples of Mexico received some new blood from the Peninsula, and even Asia (Filipino sailors manned the Spanish treasure fleets that put into Acapulco, and some Filipinos remained. The Mexican national dress is modeled on one worn by the "China Poblana", the Filipina bride of the local Spanish governor in Puebla during the Colonial period. But the great majority of Mexicans remained genetically Mexican (from "Mexica", the name of the peoples who inhabited valley of Mexico prior to the arrival of the Aztecs.)