They were no different than those slaughtered in the Holocaust, tragic victims of ignorance and hatred.
In reality Muslims were the main target of the Spanish Inquisition because they represented a disruptive enemy presence. The Spaniards had spent 700 years reclaiming the Iberian Peninsula from the Moors and needed to reestablish Christian culture and jurisprudence. Muslims did not accept the European concept of Divine Right or the God that authored it. As such they represented a treasonous presence. Remember, simultaneous to the Inquisition Islam was in a continuous and aggressive war with the Christian world. Fall of Constantinople was in 1453, the Battle of Lepanto took place in 1571 and Vienna was under siege in 1683, Greece and the Balkans were under Muslim control. Islam was a very real threat to all of Europe. One has to wonder why Protestantism remained neutral in the clash of civilizations.
The slaughter of the Huguenots was a mob action that sprang from the arrest of the Protestant leaders who were conspiring with the English and Dutch to stage a coup. It marked but a single event among hundreds in a series of populist sectarian violence incidents between Protestants and Catholics. Unfortunately, as in much of European history the peasants and poor were caught up in power politics that had nothing to do with religion.
No. The Spanish Inquisition did not persecute public Jews or Muslims. It was only concerned with public, baptized Catholics who were secretly working to overthrow church and state. Some of these public Catholics were known as Marranos, secret Jews, and Mariscos, secret Muslims. This was great problem since many Marranos had attained the rank of bishop and were destroying dioceses and religious orders. Moriscos were assisting Muslim raiders from North Africa who murdered and enslaved entire towns along the southern coasts of Spain.
On the whole, the Spanish Inquisition was a very worthy and successful Christian enterprise that took great care to guard against racial bigotry toward Jews and North Africans.
Today, many offices of bishop and cardinal have been captured by unrepentant homosexuals who work as a conscious fifth column to destroy the Church from within. Catholics desperately need to revive the Holy Inquisition as a means to restore the purity of Church offices once again.
To rid Spain of them was the strategic necessity, but the target was Jewish converts to Catholicism, who, it was suspected, sympathized with the Muslims.