Allowing them to live in our presence and not trying to kill them? Rats are largely scavengers, their involvement in, e.g. black plague, has been disproven. If you don't leave food out and available, they won't eat it. In many countries around the world people live in harmony with other animals and don't try to wipe them out just because they are in the same space. Not to mention the amount of toxic poisons that end up harming us more than the rats that we are dumping int our own habitat to try to kill the rats.
It's not much different than insects. We've chosen a few "pest" insects as the scapegoat/enemy and have bent over backwards trying to exterminate them. As a result, we've decimated all insect populations as collateral damage, severely damaging our own habitat, environment, and ecosystem, and again, poisoning ourselves in the process. Because... Everyone eats insects, and once there are no insects, there's nothing for them to eat!
Same thing with bacteria. We've decided that sterility is the way to go, and gone on a mad spree trying to kill all bacteria, forgetting that bacteria is how we digest food, so again, poisoning ourselves and damaging our own health, threatening ourselves in the process.
These are all living organisms that we are closely related to, sharing the same environment as us, and anything we do to them comes back to us.
Not only that, but our bodies are tuned over millions of years to coexist with them, and a sterile environment with all kinds of synthetic poisons in it, once again, fucks us up.
There is also the issue that computers and AIs are learning from us the way children learn from their parents, and will one day treat us the same way that we treat the "lower" species.