Supporting namespacing does not preclude having the old system too. Or from having a public repo namespace like org.pypi or whatever that allows people to upload packages to the current repo using the system they currently have. Might help sort out some of the other packaging problems too - LWN had this the other day:
https://lwn.net/SubscriberLink/923238/d48af5401c04db7d/ . Maybe it would help with the integrator notion org.conda or whatever.
Depending on how something like this is implemented, maybe com.github could set it up to pull straight from the project repo.
Just because there's ways it could go poorly, doesn't mean it will go poorly.