Conspiracy theories don't make good arguments. MS has been one of the most vocal and active in pushing for limits on and public disclosure of government subpoenas for user information.
I think you missed the key points:
1) Skype allegedly did this before MS acquired them.
2) MS never shares any private user data without a legal court order compelling them to.
3) Everything here applied to Apple, Google, and others.
This is also a very old article, and leaves out the fact that since then MS has been shown to be a defender of user privacy and government transparency.