If you RTFA, under Satya Nadella, Microsoft has been making it a point not to infect, with its own culture, the culture of the companies that it acquires.
“It would be easy for a large organization to come in and say: ‘Hey, we’re going to show you how it’s done. We’re going to get you off this Java code. We’re going to get things moved over to C. We’re going to get you off Amazon Web Services and over to Azure,’” Booty told GamesIndustry.biz. “But it’s important to realize that the conditions that created Minecraft, how it came to be, are likely to be things that are difficult to recreate within a more corporate structure.”
Mojang was the first acquisition of Satya Nadella and his decision not to touch its culture, to not mess with the magic of what made Minecraft great, proved to be very successful and it served as a template for other acquisitions such as Linkedin, Nadella's second acquisition, and six game studios that were later acquired by Xbox Game Studios under Phil Spencer. This hands-off treatment of acquired companies has been the guiding principle for Phil Spencer (now head of Xbox overall) and Matt Booty (formerly Minecraft games business leader and now head of Xbox Game Studios) in giving their new game studios free reign in developing games with minimal meddling from Microsoft.
Their eventual shift of Minecraft to Azure from AWS may have been a practical as well as a financial decision, solely, by Mojang. Aside from the obvious discount that they get using Azure, they may have priority support from Azure, if not outright being given a dedicated cloud team that focuses on Minecraft.