Image Courtesy of Vladimir Tasev (Twitter): First of all lets start by stating the obvious. Everything that Microsoft touches ends up being bent and twisted into a Microsoft product. While we embrace open source software, we also don't trust Microsoft with our proprietary private code repositories.
We all know how open Microsoft is with their own software source code so it's not hard to imaging a world in which Microsoft would be scouring the 80+ million developers code on Github for items which they could steal, copyright or otherwise lay claim to. In short, Microsoft has a bad reputation in regards to security of their own products so we can't safeguard them with our products.
We will watch to see how Microsoft handles the move. We have heard from hundreds of developers on forums we are members of talking about how bad this is for the open source community at large. We have also heard rumors that many developers have begun moving to other services and private Git repositories (which is what we did late last year even before this move).
Only time will tell if this move is the death of Github but for the time being we will secure our code elsewhere and on systems only within our personal control.