You bit off a big one!

Let me try to explain as best I can (I'm a historian of disease so you can almost trust me.)

You are correct in the basic understanding that there were, essentially, two competing understandings of disease prior to the confirmation of germ theory: the miasma theory, and "contagion," which I will put in quotes because I want to differentiate between the pre-germ theory understanding of contagion and the term as it's used scientifically.

The reason why it's kind of hard to put your finger on is that--as you are asking in the last paragraph--there was a bit of overlap between the two.

I'm going to start in reverse, which is by explaining why anticontagionism became popular in the 19th century. This debate is why a lot of people (including myself, when I first started down this path) get confused, because it seems very much like a continuation of the contagion vs. miasma debate, but it's much more polarized, and much more politicized -- and anticontagionism is not fully congruous with the miasmic theory as the latter was understood scientifically.

The debate about disease etiology (origin and spread) became very politicized with the rise of the concept of public health. Public health, at its core, is the understanding that the government (national or local) is responsible for ensuring the health of the citizenry. Why this was controversial is probably easy to understand at the current moment, given the outcry over COVID lockdowns and vaccination.

The idea had been swimming around for some time, especially since the French Revolution (the Revolutionary ideal was that healthy parents raised healthy children who would become healthy soldiers, who would then marry health women and have healthy children ... lather, rinse repeat), but with the introduction of Jenner's smallpox vaccine -- smallpox being a disease that killed tens of thousand of people every year in every nation on earth -- the idea that a centralized authority needed to get this into the hands of people took off.

And, perhaps understandably, this was wildly controversial. People were required to undergo a violent procedure (piercing of the skin and injection of a foreign substance) because the government said so. And there were huge debates about personal liberties, side effects, and all the rest (See, for example, this etching depicting wild rumors that children who were vaccinated would grow horns). -- not just in Europe, but worldwide. In Egypt, which I work on, physicians from the central health authority were run out of villages by mobs carrying huge knives (this is detailed in LaVerne Kuhnke's Lives at Risk: Public Health in Nineteenth Century Egypt) In the Yucatan, the Maya were very resistant as piercing of the skin was something that only occurred in battle or religious ritual, and doctors from the central health (with whom they often didn't have a language in common) were neither (see: Heather L. McCrea, Diseased Relations: Epidemics, Public Health, and State-Building in Yucatán, Mexico, 1847-1924).

Once this became more of a regular practice, public health authorities turned their attention to other recurring illnesses like typhoid fever and cholera, which were spread through water. The re-figuring of Paris to put in sewer lines, for example, was not without controversy, and this was done in England as well.

This all led to accusations (stop me if you've heard this, say, recently) that the government was using disease as a way to make a lot of money and exert a lot of power over individual bodies (see: lithograph of a group of doctors parading a dummy painted to look like a cholera victim).

With cholera, especially, one of the measures that was implemented to prevent its spread was quarantine, which was anathema to the British East India Company (and, after the 1857 uprising, the India Office) because cholera was believed (almost certainly correctly) to have originated in India and been spread outward via trading ships. Since the purpose of colonies was to make money, opponents of the public health overreach as well as supporters of the colonial mission both began backing the idea of anticontagionism, which basically was a souped up version of the miasma theory that insisted that disease could only occur through local conditions and could not be spread through means like trade.

And so the miasma theory was trotted about because it seemed to fit -- the idea that disease was endemic (naturally occurring) in certain geographic regions and people who lived there or travelled there just had to be prepared for the possibility of exposure. According to this argument, the occurrence of cholera in Europe in the 1830s, for example, proved that cholera was endemic (naturally occurring) in Europe, and therefore quarantining ships from India if there were an outbreak there would do nothing to prevent the introduction of its causal agent to Europe because it was already there. (It's also worth pointing out that this isn't a terrific understanding of the miasma theory, either, it's kind of a "forcing it into the right hole" version.)

This was solidly disproved in 1884 with the discovery of V. cholerae by Robert Koch and his team in Egypt, but the British dug in anyway. (This is somewhat amusing -- I'm working on an article about it).

SO. Let's get back to the first part of your question, which is about the understanding of disease etiology prior to all of this political mumbo-jumbo.

Contagion had been theorized as early as the 7th century BC -- the Indian physican Sushruta theorized about the spread of diseases from one person to another. Ibn Sina also described in in the Canon (11th century). There were great debates in the medieval period in both Christendom and the Islamic world about the existence of contagion (Justin K. Stearns' book Infectious Ideas: Contagion in Premodern and Islamic Thought in the Western Mediterranean describes this in detail).

However -- and here's what gets lost in the shuffle, and what you've picked up on -- part of the issue that theologians were dealing with was the causal agent. In other words: was there an unseen intelligent actor causing people to get sick and, if so, could this entity be God? if not, what, or whom? And was this a blasphemous idea?

For example, the following hadith of the Prophet Muhammad:

It is said that the Prophet once responded to a query from a Bedouin, “How do you explain that my camels were healthy as gazelles, and then a mangy camel comes, mixes with them, and makes them mangy?” with “Who infected the first camel?”

The question, then, was not "can one living being make another sick?" (which is how we understand it today) but rather "what is the mechanism that is causing one living being to make another become sick?"

And there are, essentially, two possible theories that needed to be examined. One is that there is an unseen force that causes the illness and transmits it from person to person--Fracastoro's seeds, but, as you've seen, he wasn't the first to propose the idea, he was just the first one to propose the idea that led to others picking up the idea and running with it. And the second is that everything or everyone that became sick was exposed to the same unseen force, possibly in the air (hence mal-aria, literally "bad air", which is the basis of the miasmic theory).

The logical approach to this question would, obviously, consider the possibility that these two are not mutually exclusive. Did each individual contract the illness in the same time and place and simply react differently (based on humoric balances in their bodies--which was a premodern understanding of what today we would identify as physiology and underlying conditions)? Or did one of the contract the disease and spread it to the others? And if so, what caused the first person to become sick?

Part of the issue here is that until the invention of the microscope--and then the identification of individual causal agents starting in the 1880s--there was no actual way to prove any of these theories. Medicine was essentially positivist: either it worked or it didn't, and if it didn't you tried something else until you got visible results. While we understand how a contagionist might view this (there's a "seed"), the miasmists had answers too, which is that toxic, disease causing fumes could come from, for example, the body of a person who had died from the disease -- it wasn't completely about geography and meteorology.

By the 19th century, most physicians were in the middle camp: it was known that, for example, drinking tainted water or bad food could cause illness, and that sometimes these illnesses could be passed on to others. It was also known that sometimes diseases such as typhus (which is louse borne) and influenza just seemed to come out of nowhere. The question was how both could be true at the same time. This is why, for example, that at the same time that the Paris sewer lines were being laid to take tainted wastewater out of the city, wide boulevards were being cut through the city to allow fresh air to circulate and carry away miasmic fumes (also to prevent barricades a la Les Misérables).

The 19th contagion and anticontagion debate took place as a layer on top of this scientific inquiry. The easiest analogy would be, for example, how medical professionals were shouted down in the earliest days of COVID by non-specialists and politicians who were taking economic or political interests into account when issuing instructions on how to prevent disease spread or cures.