I notice most of your choices start off with "Microsoft ruins...". Bias much?
I have been part of such acquisitions in the past, and in all the cases I experienced the only thing that changed was the fact that our financial info was forwarded to a head office, and some infrastructure (accountants, etc.) were allowed to transfer to other subsidiaries as their roles at our site declined.
In fact, in all cases our company heads became directors of new departments if not roles like "Chief of Research" (these were all tech companies) and everyone ended up getting promotions and/or pay raises when the deal finalized.
I can see Microsoft continuing Mojang as it's own brand with no changes while at the same time providing resources to create "Minecraft II", complete with a standard API.
Microsoft isn't blind and sees how the modding communities have extended many markets beyond their natural lifespans (Doom/Quake, Unreal, etc.) and are probably interested in that facet of the modern gaming business.