Most species that are extinct are not extinct because they pose a threat but rather by accident. Polar bears and gorillas are easily capable of killing humans and do, but we have conservation efforts to attempt to keep ourselves from accidentally driving them to extinction.

Or look at the rat. A pest animal known to have been involved in spreading diseases that killed significant numbers of humans, yet we do not seek to eradicate the species as a whole. Even mosquitoes, whom we have a similar relationship with, are not the target of some massive effort to eradicate them from existence.

Hell, even smallpox gets to continue to exist.