This is actually a really hard question to answer, although it's a good one. I'll do my best to answer it, but I'm not sure how many details I'll be able to provide.

First, I want to point out that what we (as modern people) consider rape may have been viewed differently by the people involved. Throughout Mesoamerica, marriage often had political motivations. Elite men would often marry their daughters or sisters to potential enemies in order to secure alliances. When the Spanish arrived, many native lords gave female relatives to them to have as wives in order to secure an alliance with the foreigners. For example, Bernal Diaz del Castillo describes how many of the conquistadors had been given women by the native nobility. At one point, he asked Motecuzoma if he could have a woman as well and was given one. During the very early colonial period, before the enslavement of native people was banned by papal bull, conquistadors would also take native men and women as slaves. Diaz del Castillo complains on multiple occasions that when slaves were divided up among the conquistadors the officers took the bulk of them including all of the 'pretty Indian girls,' and the common soldiers were left with very little. The implication here is that female slaves were used for sex, although it is never directly stated.

In the minds of native people, these events may have been seen as a form of marriage. You mentioned the Tarascans in your post, so lets use those as an example. The P'urépecha (the "Tarascan" ethnic group) had a form of marriage that anthropologists term "bride capture." Essentially, if a man wanted to marry a woman but would not likely be able to get her parents' permission, he could "kidnap" her and elope in secret. This was apparently a fairly common practice. Often (though not always) the bride was a willing participant, and the "kidnapping" was staged as a way for the couple to elope without seeking parental consent. When the Spanish arrived, some locals would offer female relatives to them as a way to secure an alliance, or the Spanish would simply take native women as slaves or concubines. In either case, the P'urépecha saw these actions as a form of marriage, and began using the phrase tarasque (kin by marriage, in-laws) to refer to their relationship to them. (As mentioned in that podcast, this is the origin of the name "Tarascan.") Native people also practiced elite polygyny (nobles can have multiple wives), and so conquistadors having several native women would not contradict native views on marriage.

Of course, it would be naive to think that all native people saw conquistadors claiming women as marriage, and it would be even more naive still to believe the women themselves were willing participants in this. The conquistadors, for their part, did not usually see these actions as marriage since it was not performed in a Christian ceremony and in the case of slaves they were expressly property. I am not aware of any conquistador accounts expressly describing their views on their relationship to native women they had taken, aside from Bernal Diaz del Castillo who describes it very matter-of-factly as if it were simply a normal practice. I would be interested to see someone describe Medieval/Early Modern Spanish views on marriage, sexuality, and rape, but I can't help there.

You describe the "raping and pillaging" by conquistadors like Nuño Beltrán de Guzmán. Guzmán was appointed President of the First Royal Audience (a position analogous to a chief judge) in 1528 and held the post until 1530. His expeditions into Northern and Western Mexico were infamous at the time as unnecessarily cruel, although in retrospect it probably wasn't that much worse than what many of the conquistadors were doing. The purpose of these expeditions was to acquire land, gold, and slaves. Entire towns were massacred or enslaved in the process. As I have already explained, it is suggested in some sources (although I don't know of any explicit mentions of it) that female slaves were used for sex, and so we can assume that rape was part of the numerous atrocities committed during these campaigns.

As for the second part of your question, these kinds of actions were not seen favorably by the Catholic church and many other people in Europe. While the Catholic church had sanctioned the Spanish conquests in the New World originally, many clergy that worked with native converts in New Spain quickly became advocates of indigenous rights when they saw how conquistadors were treating native people. The textbook example of this is Bartolomé de las Casas who wrote A Short Account of the Destruction of the Indies where he cataloged many, many atrocities committed by the conquistadors. There were others, however, as well. Guzman's campaigns in West Mexico (as well as the deposition and summary execution of the Tarascan monarch) drew the ire of the bishop Vasco de Quiroga who was working in the Lake Pátzcuaro Basin with native nobility that had converted to Catholicism. Indeed, his testimony against Guzman contributed to Guzman being arrested and sent back to Spain in chains. Eventually, advocacy by Catholic clergy in favor of native rights resulted in the passing of a papal bull in 1537 that forbade the enslavement of native peoples.

But within the writings of Catholic clergy against the actions of the conquistadors, rape was not a central theme. Rather, it was treated as merely one of several crimes committed by conquistadors alongside massacres, torture, enslavement, and other atrocities. The primary sources that I have read mention rape incidentally, and don't treat it as a separate accusation.

Edit:

There is a decent amount of modern scholarship on this topic, although it is very dense to wade through. The narrative of the conquistador as rapist and native woman as victim has been part of a complex discourse in defining modern Latin American identity, and most recent scholarship has focused on re-examining this narrative in a way that ascribes more agency to native women. Here are a few sources that you can dive into if you want a better treatment of the topic:

• Kellog, Susan (2016) " Alva Ixtlilxochitl's Marina and Other Women of Conquest." In Fernando de Alva Ixtlilxochitl and His Legacy Alen Brokaw and Jongsoo Lee (editors) pp. 209-234. University of Arizona Press. (This chapter isn't about rape specifically, but discusses the role of women in the Spanish conquest and Early Colonial period).

• Montrose, Louise (1993) "The Work of Gender in the Discourse of Discovery." In New World Encounters. Stephen J. Greenblatt, ed. Pp. I77-2I7. Berkeley and Los Angeles: University of California Press

• Restall, Matthew. (1995). "He Wished It in Vain": Subordination and Resistance among Maya Women in Post-Conquest Yucatan. Ethnohistory, 42(4), 577-594.