Yes, founders maybe took some money off he table, that's good for them, no question. But the company is now troubled.
GitHub has 102 employees. Which means they're already paying around $10M wage in a year and they're profitable. I bet they're at least making $20M per year right now. They're going after the enterprise market which would make them much much more cash.
Do the math. Is it really hard to pay that money back in a company like this ? Is AirBnB, Dropbox, Evernote in trouble ?
Github is not troubled.
You're correct that they haven't lost control, but now they have somebody to answer to. Somebody who just gave them $100m. Somebody with more equity than all but a few of the people involved. Somebody who's powerful and respected and whose job is to push tech companies in the direction of maximum return.
It changes things.