Will Microsoft Acquisition of GitHub affect the Future of Open Source?

No, it won't. In fact, it's going to be the opposite. GitHub had been struggling to fund itself and had no clear leadership since last few months. Microsoft acquiring GitHub fixes those problems. 

Now, with a clear vision, GitHub can continue to grow and make it more friendly for the community. It's a different Microsoft under Satya Nadella's leadership than it was under Ballmer. 

People always react negative to such acquisitions. But slowly, they'll accept it and move on. GitHub is the de-facto standard of developing open source software by distributed teams; and it will continue to be. 

I think they are going to improve their TFS by purchasing GitHub !