Is this your comic, perhaps?
I think what a lot of comments here miss is that while new tools come out that can help make things better, they don't suddenly fix people's existing installs. It seems weird that there isn't more documentation out there to help people get out of these kinds of messes.
As someone responsible for probably one of your astronomer friend's tools (Anaconda), I have to say that we can only do so much: the nature of Python itself is that we cannot ignore what the user puts into PYTHONPATH, PATH, etc. On Windows, at least, we do create shortcuts in the Start Menu to ensure that we get a well-defined command shell. But if the user forces things like PYTHONPATH, there's not much we can do to un-fsck the setup.
Maybe it would be useful to have a python-safemode (or python-portable) binary that explicitly ignores all environment variables, configuration files, registry settings, dotfiles, etc. etc. and only looks at files that are next to it in the path....