If that were something to worry about, then wouldn't OpenOffice, LibreOffice, iWork, Google Docs, etc. all be in legal trouble right now for the same thing with .doc files?
Nope because MS doesn't create .doc files, they just make the software that saves/loads them. The issue in this case is that the Minecraft textures and item geometry are created by MS (by way of Mojang) and hence MS has the copyright on them. If you replace the textures with alternative ones created by other people you're probably in the clear so far as the textures go, but the NPCs and objects geometry data is still covered.
One could maybe make the case that Minecraft's terrain generation would make your world a derivative work, but if you're building in superflat than definitely agreed.
I have no idea about the former, but if MS had any claim to a world built from scratch then Adobe would own everything ever made in Photoshop and Autodesk would own pretty much all video game content since the late 90s.
If that were something to worry about, then wouldn't OpenOffice, LibreOffice, iWork, Google Docs, etc. all be in legal trouble right now for the same thing with .doc files?