There is nothing like "the" system though. When a government launch some genocide, sure it's an expression of the system in a sense, but it didn't need to respect a majority of actor opinions, and it doesn't mean that "the behavior of the system" is a mere and direct outcome of all the social values at stake which would presumably have great safeguard against any significant deviation.

Virus can kill their hosts, and a bunch of individuals can have significant harmful impact on societies.

A virus that kills their hosts itself dies out quickly. Viruses that thrive, and that we actually have most problems with, are ones that spread before manifesting symptoms.

Much like viruses, systems are subject to selection pressures over time. Systems that are too damaging to society makes society develop memetic, cultural and legal immunity against them. Systems that let individual members easily kill them are fragile and don't survive either.

Systems that thrive are ones that are mild enough to not cause too much external resistance, and are resilient enough to not allow individuals to accidentally or intentionally break them from within.