I'm not familiar with Oldstone's exact text, but as much as I like the genre of examining history through an epidemiological (and particularly ID Epi) lens, the approach does tend to lend itself to an "everything is a nail" approach. This is not helped by the fact that these works are often written not by historians with a depth of knowledge in the many areas these overviews touch upon, but by physicians and infectious disease specialists with little to no formal training in historical methodology.

Peeking inside Viruses, Plagues and History, it seems to be an exceptionally egregious offender, at least as regards the Aztecs. Over the couple of pages on which he discusses the topic, Oldstone makes 4 general points:

• The Spanish were believed to be gods

• The Conquest was carried out by a small number of Spanish

• Smallpox allowed for Spanish victory

• The population "docilely accepted commands from the priests and Spanish authorities"

This is wrong on all counts.

The Spanish were believed to be gods

This is largely thought to have been a post-Conquest myth, used by the Spanish to signify their divine authority to take posession of Mexico. To stay on target and get to the actual smallpox, I won't rehash the arguments against accepting this notion here, but will point you instead to our FAQ section on the subject. The longevity and popularity of this myth banks on some powerfully orientalist (occidentalist?) notions, but is also buoyed along by the power of other misunderstandings of the Conquest, such as our next topic.

The Conquest was carried out by a small number of Spanish

It is true there were never more than about 1000 Spanish troops under Cortés' command during the Conquest. This tiny number accomplishing so much seems unbelievable, most because it is, in fact, not worthy of belief. By Cortés' own account he had more than 100,000 Tlaxcalan and other Mesoamerican allied soldiers at his side during the fight. The Tlaxcalans, and later the Acolhua, provided not only the supermajority of the troops of the Conquest, but also logistical support, intelligence, engineering, a base to retreat to and advance from, food, water, shelter, and basically everything else the Spanish did not have, which was quite a lot.

As such, there is no need for extraordinary explanations of how a handful of men were able to conquer a city of 200,000 plus, which had it's own allies to draw upon. The Spanish acted as heavy shock troops backed up by the major state rival of the Aztecs; one of the key Aztec groups which defected; and numerous other groups who were tired of living in fear of Tenochtitlan. This cross between interstate and civil war did not happen overnight and did not lead to an immediate defeat; there were months of battles around Lake Texcoco followed up by a 3 month siege of Tenochtitlan itself. The length of the war brings up to the next point.

Smallpox allowed for Spanish victory

Oldstone writes:

On Montezuma's death, his successor as Emperor of Mexico gathered the Aztec forces and led a night attack to drive the conquistadors out of the city. But on that night, smallpox also reached Tenochtitlan.

This is, again, wrong on all counts.

First, there was no such title as "Emperor of Mexico," the correct title would be Tlatoani of Tenochtitlan. But let's not digress into the intricacies of Late Postclassic nobility and politics.

Second, the Aztecs did not spearhead a night attack to drive the Spanish out of Tenochtitlan. They had the Spanish besieged and starving within the palace they had been given to accommodate them when they arrived in the city as guests. It was the Spanish who tried to sneak out of the city at night, several of their previous break-out attempts having failed. This led to La Noche Triste in which a significant portion of the Spanish forces were killed as they fled the city. An Aztec force did pursue the Spanish as they retreated back to Tlaxcala, and was soundly defeated at the Battle of Otumba. At that point though, the Aztecs had basically achieved their aims of getting rid of the Spanish and were focused on settling internal dissension and shoring up the position of the new tlatoani.

Third, this is not when smallpox arrived in the Valley of Mexico. The epidemic started on the coast, where it had been introduced with Narváez's forces, and spread inland over the course of months. Per Sahagún, the Aztecs celebrated a feast in the month Huey Tecuilhuitl, roughly around July. The epidemic did not occur until Tepeilhuitl, roughly October. The outbreak lasted for about 60 days, dying down in Panquetzaliztli, roughly December.

The epidemic was quite devastating, with estimates of up to 50% mortality in some areas of the Valley of Mexico. Bizarrely, the primary source Oldstone quotes from in order to illustrate this impact comes, not from an Nahuatl (Aztec) writing, but from the Annals of the The Annals of the Cakchiquels, a Maya work. Regardless of odd choices in quotations, one of these deaths was the newly elected tlatoani, Cuitlahuac, who was replaced by Cuauhtemoc.

Had Oldstone chosen to focus on the political ramifications from the epidemic as being a factor in the Conquest, he would be within the bounds of modern scholarship. The election of a new tlatoani always meant a period of political disorder as conquered polities started to get the idea that now might be a good time to stop paying tribute and political rivals contemplated whether now was their opportunity to make a play for putting themselves in charge. So the death of two tlatoque in the space of about 3 months was a significant blow to political stability. Smallpox also swept through Tlaxcala, leading to the deaths of several key personages there, which allowed the Spanish to use their influence to put Spanish-friendly Tlaxcalans in positions of power.

Oldstone instead focuses on how:

The only interpretation [of the epidemic] obvious to [the Aztecs] was that they were being punished by angry gods. It seemed the Spanish god was supreme over the Aztec gods, just as the Spanish conquerors came to dominate and obliterate their Aztec foes.

There are, again, more than a few problems with this interpretations. The first being that the Aztecs did not actually see the Spanish not being affected by the smallpox epidemic (notwithstanding there being some brief mention of sick Spaniards as well). The Spanish were holed up in Tlaxcala, and while they carried out attacks on some towns outside the Valley, did not re-enter Mexico proper until after the epidemic had already subsided.

Second, it is a huge and demeaning misinterpretation of the nature of Aztec religion and philosophy. Contrary to popular belief, people in the past were not idiots, and were capable of responding rationally to disasters. Pre-modern people did not have the strict dichotomy between the natural and supernatural as the modern world, but that doesn't mean they flocked to the god du jour with no other option in times of distress. I wrote a bit about how a mid-15th century drought was dealt with by the Aztecs which touches on this topic.

Third, on the topic of that rational behavior, we have post-Conquest texts that collected Aztec medical knowledge and we have writings that illustrate the detailed approach they had to health and the body. Mesoamerica may not have had the communicable disease endemic to Afro-Eurasia, but it was not without illness. It is a baldly ethnocentric position to assert that Americans would not approach the outbreak of an epidemic as the thing it was, a disease.

Finally, Oldstone engages in tautological reasoning to assume that the Aztecs were conquered because they held the Christian god as superior to their own, when they had not yet been conquered. The Spanish began their assault on Mexico in late December 1520. It would not be until August 1521 that Cuauhtemoc would finally surrender, and the months between were filled with constant pitched battles. If they Aztecs were going to submit to this powerful god of the Spanish, they had a strange way of showing it. Which bring us to the next point.