"route everything through government surveillance" is perhaps a bit too blunt, but let's not forget that Microsoft was the founding member of the PRISM program.

And Prism or no Prism-- Skype was a $1bn present from Microsoft to the intelligence community. Even if they never snooped on anything (we know they have) they did re-engineer skype in a manner that allows it to be subject to more traditional CALEA trap and trace techniques, as well a numerous side channel attacks and traffic interception. The "secret sauce" of Skype in the very beginning was P2P connections, which MSFT immediately removed.