This reminds me of 2010, when Stephen Elop was hired as the CEO of Nokia. Us Linux folks knew immediately that based on his past actions at Microsoft, Nokia's Linux development would be killed, Nokia would move to Windows Phones, and because they won't sell (Microsoft has only ever been able to compete as a monopoly), eventually Nokia would be in such a bad state Microsoft would buy it. Everyone called us conspiracy mongers, tinfoil hat long-haired smellies, and whatnot. Yet, we were right, on every single point. Even if "analysts" afterwards claimed that no-one could have predicted it..
It is not because there was a conspiracy or anything, it was because that is the way Microsoft (and officers hired by Microsoft, pun intended) operates. Whatever will become of Github, it will be twisted just like everything else Microsoft acquires. Ignoring the past behaviour of the company is just sheer idiocy.
If you're a happy Microsoft customer, then good for ya; you probably won't be burned by this. Everyone else should consider the purchase price, past Microsoft behaviour, and draw their own conclusions.