What was Agent Smith in "The Matrix" referring to while torturing Morpheus?

Context

Smith is being quite on the nose about what he means. This isn't some indirect allegory about religion, race or specific historic events, as you're suggesting with your question. Smith is explaining exactly what he says.

Before we get into what Smith means, you have to keep three things in mind:

• Smith is built for a specific purpose, and that purpose is inherently anti-human. There is no guarantee that Smith has been constructed with the capability of grasping the bigger picture (and it is later revealed that there are many things he never understands that other machines do).
• Smith really hates humans (exceptionally so, if you follow how his plotline resolves in the trilogy)
• Smith is intentionally trying to rile up Morpheus

Therefore, Smith's observation is not only biased from the get go, it is a partial observation and likely also exacerbated by him trying to anger/annoy Morpheus. The below "truths" I state are truths as Smith represents them, I am not discussing factual correctness.

Smith's arguments

Animals tend to synchronize with their biotope. Their numbers may increase and decrease, but the biotope generally remains functional, barring some unexpected outside event. There's often a "circle of life" chain going on in this biotope, where each animal contributes to the biotope and keeps it alive.
This "circle" means that things stay more or less the same.

Or, as Smith puts it:

Every mammal on this planet instinctively develops a natural equilibrium with the surrounding environment.

Viruses, however, do not take care of their biotope, i.e. the host in which they grow. Viruses generally attempt to kill or otherwise damage their host. They may keep a host alive long enough to spread the virus further, but that doesn't last and eventually the virus will consume the host.
The main thing I'm trying to point out here is that for viruses, things irreparably change (i.e. killing their host, hoping to find a new host to continue living).

Or, as Smith puts it:

You move to an area and you multiply and multiply until every natural resource is consumed and the only way you can survive is to spread to another area.

He's referring to humans in this quote, but the end goal is to argue that this is analogous to viruses.

So now let's look at humans, who have effectively ravaged the planet they live on. Things aren't the way they used to be, and they don't seem to be getting better, and therefore there is no "circle", no equilibrium. Humans are using up resources without contributing to the reparation of that biotope.

In that observation, humans irreparably change their biotope (i.e. Earth), and have not been able to find an equilibrium.

Smith therefore argues that humans are a virus. And since humans understand that viruses are bad and should be avoided/eradicated, Smith is trying to get humans to agree that humans should be eradicated, using humans' stance on viruses against them.

I mostly picked on ecologism because it's the closest match to Smith's argument, but Smith's argument effectively applies to anything caused by humans that we have since come to deem as evil or unsustainable. Some of the things you mention apply as well, but Smith is not pointing out anything in particular. He's discussing humanity in broad strokes.

Corrections

I can't help but correct Smith here:

• Not every animal finds an equilibrium. It's just that those who don't eventually die out as their non-renewable way of living inherently doesn't persist. Because if it did, then they were living sustainably and thus would have found that equilibrium.
• Animals don't find an equilibrium, as they don't understand the intricacies of the biosphere around them. Animals luck into an equilibrium, either by evolving into it or just random coincidence. Those that don't luck into it go extinct.
• Smith is built to maintain the "zoo" that is the Matrix. The machines specifically want to keep the humans around. Smith's argument effectively contradicts his own purpose. This is further explored in later movies but the main takeaway at this point is that Smith is wrong even by machine standards.
• The machines aren't particularly contributing to Earth either (as far as the trilogy ever explores), so Smith's argument is severely hypocritical. The Machines are kept alive purely by the grace of being able to harness human body heat, so the machines are at least as much of a parasite as Smith claims humans to be. They keep humans around just long enough to suit their purpose (i.e. power generation), but otherwise discard humans at every turn. Sounds an awful lot like the virus Smith just described.

It is unclear how much of Smith's statement is either genuine misgiving, racial stereotyping, or disingenuous rhetoric in pursuit of his selfish goal of exterminating humans. FWIW, he seems to genuinely believe what he says up until the very end.

Based on the initial discussions, I will briefly summarize our understanding of how actual viruses work, thereby revealing Agent Smith to be actually less than your everyday villain figure, and - while not giving a conclusive answer - offer some food for thought and hopefully trigger some more interesting interpretations!

Scientific facts:

• Natural viruses have co-evolved with cells, exist outside as well as inside of cells, and contribute to evolutionary processes
• Viruses aren't sentient beings, they are glorified instruction sets for the cellular transcription and translation machinery and have no intention, hope, agency, morality, responsibility etc.
• Diseases can result from infections, but again, there is no intention, hope, agency, morality, responsibility etc. "behind" a disease (contrary to what certain, e.g. religious or political institutions might preach, politicizing suffering and misery as well as the experience of healing and death/salvation)

Storyline facts:

• Humanity has been enslaved by her own creations, machines and AI that have gotten out of control by misuse, rapid evolution, and unlimited energy supplies
• The Matrix is a "neuro-interactive simulation" (as Morpheus explains to Neo on his first time in the Contruct), a neural world existing on top or within the "desert of the real"
• Agents (= also a software engineering term) are pieces of code and part of the Matrix as Neo will come to see: A cascade of numbers and symbols

Important implications:

• The "neuro-interactive" Matrix and the Agents therein (the software) belong to the realm of the mind, the machines (the hardware) belong to the physical reality, while humans (the users) live and die (can be killed!) in both worlds
• Classifying Smith's own behaviour of resource consumption and uncontrolled replication, he himself is a virus ("a rogue program")
• Being a virus - his humanoid appearance hardly conceals his machine nature - Smith has no intention, hope, agency, morality, responsibility etc. and therefore he cannot be judged according to moral or ethical norms
• Being programmed into the Matrix, Smith is a virus of the mind, contrasting the machines that created him (which represent hardware viruses and mechanized organisms)
• Being a virus of the mind, Smith infiltrates the mind and replicates within, modifying human behaviour and eliciting fear, treason, exploitation, and murder - pitting humans against humans
• Though Agent Smith's behaviour is hyper-aggressive and destructive towards the human characters, his observations are surprisingly not. There is no personal grudge in his view and his description of human behaviour as virulent is just that - descriptive. Ironically, he inevitably describes himself - but being ultimately a human creation, irony becomes tragedy. Conversely, the audience's antipathy towards "him" is on a fundamental level irrational: The actual destruction and enslavement has already been initiated by humans and concluded by machines a long time ago.

... Interpretations?

• So what are possible references for Agent Smith's character (a virus of the mind) and what he observes as virulent, destructive behaviour (the disease)? What is our Matrix? Who is our Agent Smith?