If Microsoft can somehow manage to gain trust from Github users, which is very possible and desirable for them, it will make Azure more compelling in many ways than Amazon as a cloud computing platform.
After Amazon's acquisition of Cloud9, Microsoft is the first big company to try something really bold and inventive in cloud computing. Github can prioritize making code deploy to all clouds AND make it especially appealing for customers to choose Azure, as there will exist amazing opportunities for end to end product optimizations here. Seems really smart for me, and given that Microsoft is really hell bent on changing people's negative opinions about them, they have all the right incentives to make Github even more awesome than it already is.