I don't think this is really a plan to destroy Windows. Sounds more like they're just working on the open source OSs because it's easier to do while the Machine is still largely theoretical. If it does ever come to market, I'm sure they'll end up working with Microsoft in some form to create something together. But that requires all sorts of legal business agreements, which you can completely avoid in the early stage…
Anyway, what kind of a market would there be for Windows in this market? There's a Windows supercomputer OS but it don't think it's used much, for example.