It seems pretty murky and contradictory at first glance - almost impossible to infer what he actually thought.
I would argue that the answer is neither. You are certainly right that his writings are quite murky; he is an incredibly complex figure who continues to be heavily studied today. He was a prolific writer, theologian, and legal scholar in a period that completely altered the trajectories of societies worldwide. But Vitoria’s goal at the time of his writing was neither to defend nor criticize the Spanish Empire itself. Instead, his scholarship was more concerned with the new questions bubbling forth from the (then) modern world.
To better understand his views, we should contextualize his writing in both the history of the period and Vitoria’s education. The period during which he was writing was one of the most revolutionary in European history. Spain inadvertently stumbled onto two continents filled with millions of creatures, some of whom seemed very human-like. These beings possessed cultures, social structures, and mores drastically different from sixteenth century Europe. Yet right from the outset, this “new” world was set upon by adventurers who often seemed to conquer and pillage first, then find the legal justifications for doing so later. In the process, many, including the Crown and the Papacy, were enriched both spiritually and economically. Yet alongside the initial violent collisions between these two worlds, debate raged throughout the empire about how to incorporate this new, radically different realm into preexisting European understandings of how the Earth and its people worked. Simultaneously, Christianity seemed to be coming undone, with more and more religious conflicts exploding across Europe, unleashing both violence and a torrent of new social thought.
This was the environment in which Vitoria grew up and was educated. As a young man, he studied classical and modern philosophy, especially Thomism and humanism, which imbued his sociopolitical discourses with critical undercurrents. He was also shaped by the idea of natural law, which had a lengthy, evolving history that would have been known to classical scholars at the time. For Vitoria, natural law dictated limited exertion of the state over the individual and corresponded to the first inklings of international law and human rights (both of which would, of course, come to have very different meanings than they did during Vitoria’s life).
Viewed in this context, his writing makes more sense as trying to rectify these diverse philosophies with the events taking place in the world around him. For example, based on his own philosophy about the limits just war, Vitoria rejected how conquistadores and the Crown waged war on indigenous peoples of the New World, saying: “Unbelief does not destroy either natural law or human law; but ownership and dominion are based either on natural law or human law; therefore they are not destroyed by want of faith.” In the process, he rejected the tradition that whatever the king or the pope says goes. He also takes a somewhat uncommon stance in arguing that indigenous people were fully human, capable of reason and personality, and therefore possessors of natural rights. It sounds ridiculous to us, but at the time, Europeans were absolutely perplexed by the extent of humanity that indigenous people possessed. Another example of criticism that he levels against the monarchy would be the complicated relationship between the individual and the state. According to Ramón Hernández, “to Vitoria, in nature lies the efficient cause and primary origin of all power, be it physical or moral, personal or social, or private or civil. Each of these different dimensions of power flows from the same condition of human nature, and ultimately each must be attributed to the creator of this nature who implanted these inalienable conditions within it” (1043). Therefore, Vitoria pronounces certain rights that individuals maintain that exist outside the absolute authority of the king. For pronouncements such as these, the Crown strongly condemned his writing.
Though he levels criticisms at the Spanish Empire, he often rectifies these ideas to justify imperial actions, which from a modern perspective seem contradictory. When discussing war with indigenous people, he argues that the King could wage war on indigenous populations when the natives broke natural law (which included religious violations). The initial conquests may have been illegal but subsequent wars predicated on attacks on clergy or travelers were just wars. These two positions seems contradictory today, but by standards of sixteenth century philosophy, they successfully reconciled the questions at hand by rejecting some justifications rooted in older law and replacing them with those of natural law. Additionally, Charles V wrote to Vitoria on multiple occasions to ask for advice. He sought comment on the divorce of King Henry VIII, sending missionaries to New Spain, and other questions about indigenous rights. So although the monarchy disagreed with some of his points, the Crown also accepted his preeminence as a thinker and legal scholar.
Therefore, we see that his writing was not concerned necessarily with criticising the Spanish Empire itself so much as he was concerned with answering questions within the Spanish Empire. To answer these questions, he sometimes criticizes and other times supports dominant political, social, economic, and philosophical discourses, drawing on extensive philosophical and legal precedents borne out in the Renaissance/early Enlightenment.
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