I do not know much about minecraft mods but I still seem to remember they are Java as well. If they port minecraft into MS tech (DirecX and C# presumably) what happens to the community mods?
Probably DirectX and C++. And in fact, Microsoft would most likely buy some other game which is close to what they want, then task the studio with making it into Minecraft 2. There are loads of Minecraft clones out there, the trick is finding one which is both technically competent and developed by someone willing to work for Microsoft and sell them their baby.
The existing mods wouldn't work with the new game, obviously. But many Microsoft games have been modded fairly extensively, and Microsoft has even released the sources to one of their games when they were done with it (Allegiance.)