Out of the box, Chromebooks are really not intended to do much other than consume web-based content, including sites like CodePen or other web-coding interfaces. It seems like you've explored those options fairly well.

If you can't modify the machines to run full Linux environments (ala crouton), you're mostly stuck with web-based experiences, or the apps provided to you by the Chrome Web Store.

Teaching your students to SSH into a Linux box and teaching them basic BASH skills is pretty worthwhile in itself. You seem to have made the best of a quirky situation.