I don't really see how this is a bad thing. They were very much profitable, and were likely able to dictate the terms of the deal. Also, the money came from one of the most, if not THE most, reputable and respected VC firms.
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.
The founders (probably) achieve some liquidity, the company gets to expand up and out in the market, with the guidance of some of the most experienced investors in the business, the customers get see more resources put towards what is now a very large product, and the investors get to ride the wave that I think will see GitHub reach a few billion dollars valuation.
That helps explain why the founders sold the equity, but not why the VCs bought it.
Company with a proven modal, proven team, proven management and a massive growth opportunity (company hosted Github).
(I considered deleting my comment, but my hand was stayed by its having gotten an upvote.)