Now I know absolutely nothing about internal MS politics. My immediate suspicion, based on how MS seems to operate, is that's code for "won't bow down to Windows/Office".
I really hope that's not the reason. There have been so many times Microsoft seems to be unable to get out of its own way because they have integrate Windows/Office into something somehow. Maybe he was part of that problem, but the fact us was involved in Windows 8 makes me doubt it since they were willing to make radical changes (good or bad).
If I had to guess, I'd put money on the lukewarm Surface reception being a final straw. The timing seems too perfect.
The article is suggesting that Sinofsky is the kind of person who did not, and that a less contentious person could have done an equally good job without alienating other senior leadership.