2FA isn't a solution to security, it's a solution to hinder and dissuade low-effort hackers from compromising accounts - it's still subject to social engineering (like spearphishing).
I tend to agree with your broader point - sandboxing will be the way to go, I've been having that very discussion today. we're also now enforcing CI pipelines with pinned dependencies (which we do with our helm charts, but npm by default will install with ^ semver and putting that on the developer to disable isn't good enough - the problem of course is that requires the OS vendors to agree on what is common.
This is a riff - not sure how possible this is, but it's not coming from nowhere, it's based on work I did 8 years back (https://github.com/takeoff-env/takeoff) - using a headless OS container image with a volume pointing to the source folder, run the install within the container (so far so good, this is any multi-stage docker build)
The key part would be to then copy the node_modules in the volume _data folder back to the host - this would of likely require the OS vendors to provide timely images with each release of their OS to handle binary dependencies, so is likely a non-starter for OSX.