It's better to think of these kind of systems as Disposable infrastructure instead of Immutable infrastructure. The difference being is that you occasionally, temporary can accrue some state on a machine (eg: debugging, hotfix), but you are accustomed to the idea that you can indiscriminately dispose of any system without worrying about state present on the system. So after you're done debugging, you just throw away the system and have a new replacement build automatically (by autoscaling or similar systems).

Managing NixOS system is an organizational pain in the ass. Virtually everyone knows Ubuntu. Virtually all vendors provide some sort of standard supported deployment like Docker or Ansible. Now anyone who’s affected by a NixOS deployment either has to spend months learning Nix or escalate to the a handful of gurus.

I don't think there's anything that stops you from doing that? You can edit the running system the usual way AFAIK. Even better, afterwards you can just reset the box and all your changes are automatically cleaned up.