If they are unable to use a shell, don't understand environments etc. I would push them onto some specific IDE/plugin combination that creates a new virtualenv, handles PATH etc. for every new project.

Dealing with environments and understanding how different parts of the filesystem relate to each other is its own pretty steep learning curve. You wouldn't want them to get tripped up on that while they are learning to program, so I think I would opt to teach the two as entirely different concepts and not mix them at first.

No idea if an appropriate IDE/plugin combination exists! Surely there is one.