repl.it is a great site with REPLs for a bunch of different languages.
You certainly can use Atom to develop in Python, and I would happily regale you with its features and how good a learning tool it can be, but your initial assumptions seem to have Atom doing more than it does out of the box. It can be made to do almost anything, but that requires someone to develop a package for that thing.
Python is a relatively easy language to learn, and I would absolutely recommend it for most people learning how to code, but most six-year-olds are still working on literacy in their primary language. Unless she’s hyperlexic and takes to the coding really easily, you’ll have to wait a number of years before her brain is developed enough to grasp the abstractions represented by all the punctuation. This is why I recommended Scratch: it uses shapes and colors to communicate the function of its statements, and it doesn’t let you put things in an order that won’t work.