Microsoft will absolutely screw this up. We shouldn't forget why Minecraft became popular: It was run by one (and later a few) guys who were close to the community. They cared about input and made stuff to be fun. They avoided all kinds of big business/management decisions to taint that or get in the way.

There is no way Microsoft will let it run like that. They bought it because they have plans for it and those plans will likely collide with the interests of the community. Microsoft is big in the gaming console business and struggling in the mobile market. It seems likely that they'll try to use Minecraft to push those markets.

Even if they won't do it immediately I suspect that they'll eventually make Minecraft exclusive to Xbox and mobile. Meanwhile they'll drop or decrease support for systems they don't like, like GNU/Linux, Playstations, etc. Maybe this will be part of a rewrite or a new huge upgrade (which I guess we can call "Downloadable Content" or whatever it is called in the XBox universe from now on).

And Microsoft will put their game guys in charge of it. And those guys speak a different language than Mojang. They don't care about indie and close community. They care about downloadable content and making new sellable releases every 12-24 month.