Which of those answers do you prefer? Accepted one seems a bit far fetched and simplistic. As Tatiana notes: "SharePoint is .NET, and it's half of Office.". Also see Larry's comment.
I'll warn in advance that this is the jazz hands answer, because it's really impossible to tell. I doubt any one person decreed WinRT should be native; most likely it was the best of many compromises. Anyone willing to name names while documenting the internal politics that went along with the decision(s) could write quite the page-turner!
* I could see decisions being influenced by long-term career prospects, but believe that people would be smart enough to hide most of this by working harder to find evidence supporting the direction they needed the tech to go.
* According to my limited understanding, Microsoft long ago threw out a bunch of OS-level managed development pre-Vista (WinFS-type stuff) in part because of performance related issues.
* ASP.NET (SharePoint) / managed code server-side is not going away any time soon, if ever... it's just too easy (and server hardware can typically handle any overhead).
* .NET client-side could go either way; I think this is what the accepted answer is saying (eg. Silverlight as this decade's VB6 - convenient LOB tool killed with no direct transition to new tech)
* Mono/Unity 3d/etc. are wildcards here, particularly as they support C# for non-Microsoft platforms (especially iPhone/Android).
* Microsoft, or at least powerful people within Microsoft, love COM (one of my least favorites, but I don't deal with cross-language runtime/binary compatibility).
I found this StackOverflow link on a huge discussion of the death of Silverlight, saying it was the first casualty of a "death to managed code" campaign: http://forums.silverlight.net/post/612643.aspx
The highest voted answer is clearly the sensible interpretation, but people do like to indulge in gossip and the 'politics' answer pushes those buttons.
