The article begins by discussing their choice to open source an integral part of their product. The article ends with an admonition: "Don't open source anything that represents core business value." It seems like Grit certainly represented core business value, yet they open sourced it. I'm guessing that what they really mean is that you should open source almost everything that represents core business value, but one…
If somebody found the code, would cloning your business be the obvious thing to do with it?
This isn't true of Grit. It is true of the core GitHub app, and it is true of the GitHub Jobs app.
Interacting with Git from Ruby is not the core business value of GitHub. It's just something GitHub does in the process of providing its real core business value, which is the awesome interface and collaboration features they've built on top of Git.