He said that the Windows Store was a "catastrophe" because it would make the whole OS closed source. Lots of journalists (real ones) said that it was a radical statement to only make his new competition look bad, which makes more sense than Microsoft ditching their decades of tradition and closing their OS over a new store competing with Valve.
More sense than microsoft wanting to take a cut of every piece of software sold for windows?
I don't have the answer, but if it were me, and I was the billionaire MS CEO, I take the gamble because the upside would be E-N-O-R-M-O-U-S
PS they have no problem doing it on the xbox platform, so I'm not sure of what 'tradition' you are speaking of.