I don't begrudge Notch and Mojang as a collective being sold to Microsoft. It'll only be a problem if Microsoft does things like not allowing mods on the PC version or trying to take all revenue generated from Minecraft LPs or something. No, in all honesty Notch has shown the general thing about Capitalism: make a product, and then sell it.
The only thing I find "wrong" about any of this is that Micrsoft made a terrible investment. 2.5 billion is way too much to spend on a company that has made 1 successful game. Sure the merchandise is there, but it'll eventually dry up. Look at Rovio and Angry Birds. Not to mention this purchase was apparently to be to try and increase sales of Windows Phones, which is even dumber if you as me. Then again, over the past few years I've seen ludicrous amounts of money being spent on things they could have gotten for less. Then again, nothing beats the Facebook and their 19 billion acquisition of a damned app...