That's a foolish waste of $2.5B. At least with Nokia, Microsoft weakened them significantly before outright buying them out. With Nokia, the hardware development was what's valuable. That's why they're getting rid of the brand, and why Elop switched to Windows Phone so easily.
With Minecraft, the brand itself is the only real valuable thing. The code itself isn't worth terribly much, considering it wasn't too well-written, and the game itself is not hard to clone (Minecraft itself is a clone of a game). The few Minecraft-only mobs (creeper, enderman, etc.) are really the only bits of the game worth money, and even then, the mobs are much more valuable as brands than as code.
The ecosystem (mods, modpacks, texture packs, etc.) taken as a whole is worth a ton more. But Microsoft doesn't have a very good track record of managing their communities, so I imagine they'll eventually squander that. Hell, I'm pretty certain most mod devs are already thinking of where to move their stuff next.
Throwing devs at the mod API and getting it out the door (after what, 3 years?) might help with the exodus, but that'd be a stopgap measure. People probably won't leave limbo until Minecraft 2 comes out, and at that time, we'll finally know what direction Microsoft's going to take the game. But by then, most mod devs are probably going to be long gone.
Anyway, to your point, Minecraft wasn't really competing with Microsoft. Yes, its ability to run natively on Mac and Linux is a bit of a thorn, but the fact that it runs on Windows as well makes it less so. The lack of a version for Windows Phone (and Metro) was also annoying, but it's really one very, very small drop in the bucket of problems with that whole mess. There's a version for XBox, so it's not like Microsoft was missing out on anything there. Microsoft isn't going to pay $2.5B to make an incidental (at best) competitor go away. They have to have plans for the purchase, bigger plans than just bringing it to Windows 8 and Phone.
What those are, and whether they'll be any good, well, time will tell.