Ironically, this happened because of a mitigation put in place to prevent the leftpad disaster from happening again. To recap: the developer of leftpad removed his package, which broke packages that depended on it. To prevent this from happening again NPM decided that you can't unpublish a package that has dependents, which I think is a sensible policy. The result of this is that you can prevent anyone's package from being unpublished by depending on it. This 'everything' package simply took this concept to its extreme conclusion.
Personally, I think if you're not sure you want a package to be available publicly in perpetuity, you should maybe consider publishing it to a private registry. Even if NPM did allow developers to unpublish any package, there's nothing stopping me from downloading a tarball of your package as soon as you publish it, and hosting a mirror of it somewhere else.