So Rafael Rivera made a blog post about this, claiming that Notch might have misunderstood why Microsoft contacted him. According to him all they asked Notch to do was to certify Minecraft so that it could be listed in the Windows 8 Store. Listed as in only displaying a link to www.minecraft.net. Nothing more, no app hosted by Microsoft or anything. Not converting Minecraft to an Metroapp. Just a link.
I guess we don't know until Notch clears this up, but if it is true then this news article is wrong and most comments are wrong as well.