There was no substance behind that. It was just a poorly managed PR disaster. One of many during that year that Windows 8 was launched.
Silverlight deserved to die. But somewhere along the line the Windows division got the wrong end of the stick and thought that meant all of .NET too.
They've stopped the rot now between the DevDiv and Windows divisions. Heads were banged together over that one. Sinofsky was blatantly behind it, that's why he got sacked. It wasn't about Windows 8 not being a good product (it was). It was because he was running the show like Steve Jobs did in the 80s; actively fostering mistrust between teams and undermining intra-division communication and respect.
I don't think the Windows division will ever fully respect .NET for what it is until some of the old guard have moved on. Which is a real shame. It is a first class programming stack that is practically unrivalled.
No, that was just a big scare. Microsoft dropped Silverlight (browser plugin to run sandboxed .NET apps in the browser) in favor of HTML5+JS, but I think that was an eventuality anyway as Silverlight never really seemed to gain enough momentum to stand on it's own merits.
I think the point is that there are now multiple officially sanctioned ways to develop apps for Windows Phone and Win8 tablets: .NET (C#/F#/VB.NET/etc.), WinRT (C++/CX, which is an offshoot of C++/CLI), and HTML5+JS. Each way has it's own strengths and weaknesses, but the idea is that you can use whatever's best for your specific application.