I think the point around incorporating MFA into the automated publishing flow isn't getting enough attention.
I've got no problem with doing an MFA prompt to confirm publish by a CI workflow - but last I looked this was a convoluted process of opening a https tunnel out (using a third party solution) such that you could provide the code.
I'd love to see either npm or GitHub provide an easy, out the box way, for me to provide/confirm a code during CI.
I'm feeling that maybe the entire concept of "publishing packages" is something that's not really needed? Instead, the VCS can be used as a "source of truth", with no extra publishing step required.
This is how Go works: you import by URL, e.g. "example.com/whatever/pkgname", which is presumed to be a VCS repo (git, mercurial, subversion, etc.) Versioning is done by VCS tags and branches. You "publish" by adding a tag.
While VCS repos can and have been compromised, this removes an entire attack surface from the equation. If you read every commit or a diff between two tags, then you've seen it all. No need to also diff the .tar.gz packages. I believe this would have prevented this entire incident, and I believe also the one from a few weeks ago (AFAIK that also only relied on compromised npm accounts, and not VCS?)
The main downside is that moving a repo is a bit harder, since the import path will change from "host1.com/pkgname" to "otherhost.com/pkgname", or "github.com/oneuser/repo" to "github.com/otheruser/repo". Arguably, this is a feature – opinions are divided.
Other than that, I can't really think of any advantages a "publish package"-step adds? Maybe I'm missing something? But to me it seems like a relic from the old "upload tar archive to FTP" days before VCS became ubiquitous (or nigh-ubiquitous anyway).
Publishing a package involves 2 phases: uploading the package to npmjs, and making it availble to users. Right now these 2 phases are bundled together into 1 operation.
I think the right way to approach this is to unbundle uploading the packages & publishing packages so that they're available to end-users.
CI systems should be able to build & upload packages in a fully automated manner.
Publishing the uploaded packages should require a human to log into npmjs's website & manually publish the package and go through MFA.