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This is the point - smallpox functions well on its own, it just happens that humans prefer bodies that are "living." Hence, doctors try to limit the spread of the disease to meet their health preferences. Whether this is ultimately beneficial is an ongoing debate.
I would point out that in many cases enforcing artificial health on people can have negative outcomes. Recently, the Ebola virus in Africa killed several thousands. If the sick had been allowed to immediately die without care, the disease would not have spread so far. It could be said that attempts to regulate "living" into people merely leads to a masking of human frailty, which can be very dangerous.
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Maybe a slightly less offensive comparison on my part would have been wildfires. They do just fine without human intervention. And yes, maybe humans do intervene too much. But gee, we like our houses to not be on fire. That doesn't mean we let the fire just burn, though.