All they did was take down the website that links to the GitHub repository. They already tried to have GitHub pull it, and they did but then restored it and setup a legal defense fund for projects in similar situations which seems like a pretty big "fuck you".
This story is a nothing-burger, the equivalent of the blue bucket meme.
This seems like it would follow along the same lines as emulators and torrent downloaders. If you don't download anything illegal with it, you're not doing anything wrong. I use this software for work to download good resolution/low filesize copies of my client's videos. Hopefully I can continue using it.
I don't even think you need to go as far as comparing it to emulators and torrent downloaders. It just downloads what's publicly hosted on the web, it's no different from a web browser basically.