From Engadget's article
Sounds like Notch was ready to sell. Microsoft simply took advantage. Can't be mad at that. Plus, I'm hearing estimates that Microsoft will make that money back in roughly 10 months. Not bad for a game that likely has years of life left. In the end though, nothing really changes except Minecraft on more Windows devices.
IMO, the studio still needs to diversify. They wouldn't even have to abandon Minecraft, not with all that money in the bank. They could have several high profile games going at once (though I'd rather see them work on one great game). They could even do the opposite; make several small indie games and see what catches fire. Then, much like Minecraft, exploit the hell out of it.