I agree. Sorting huge, multinational, publicly traded companies in friends and enemies list is so obviously bogus and immature that it baffles me that this is so prevalent.
Microsoft is not your enemy. It's not your friend (unless you're one of the shareholders). It's profit driven and amoral. They'll always line up with whatever they believe will maximize profits because that their entire reason for existing.
Apparently Microsoft decided that being more FLOSS friendly (after decades of trying to annihilate these projects, lest we forget) because they decided that it would favor them in the long run.
If they ever decide that they stand to make more profit by throwing the whole github ethos under the bus they will. A few people will make strongly worded blog posts that will reach the top of HN. A few employees might even quit and loudly slap the door on the way out. Then probably nothing will happen.