I think the surviving humans should be viewed as part of maintaining a healthy immune system. The Shoggoth are the white blood cells - aggressively destroying threats and the zombies are like antibodies - swarming towards foreign matter and potential infectious agents. But to have a healthy immune system you also need exposure to varied threats as if your environment is too clean then the immune system can weaken or end up fighting the wrong things. The place of the few surviving humans in this is as a controlled exposure to basically harmless threats. We are, in effect, vaccines keeping the blob ready for any potential serious hazard. (Hazards on the level of the Reapers or Borg).
That also explains why zombies keep evolving and humans get access to mutagens. Our fake-threat can’t be too easy or we wouldn’t be useful and the blob keeps automatically developing new and improved ways of fighting off potential problems.
But if we ever get TOO good the blob can probably just wake up enough to flip the big self-destruct switch as we are all basically infected anyway.