Considering how interested Microsoft has been with creation tools aimed at children with Kudu, and all ages with Project Spark, it makes a lot of sense that Minecraft would be something they'd desire. Not in the 'lol MS wants their own LBP clone,' but something bigger.
Minecraft has some really clever creation elements with the various switches and contraptions you can do within the game as it is. Imagine if MS inked a deal with schools across the world to put a more educational version of Minecraft into classrooms? Then you have the "real" game for personal use on just about every platform, merchandise deals, and animated movie rights...
That all seems more valuable and in line with the service-focused, software nature of current Microsoft than Minecraft 2 exclusive to Xbox, 'takin' away muh mods,' micro-transactions, or whatever.