As pointed out elsewhere, npm also already supports scoped namespaces: https://docs.npmjs.com/misc/scope
...and has for almost a year:
> (As of 2015-04-19, the public npm registry does support scoped packages)
The right path forward probably involves encouraging major packages (e.g. https://www.npmjs.com/browse/depended) to move toward scoped package names, and then eventually deprecate non-scoped names.