you are misleading the people , Cyanogen is NOT an "its own version of the Android mobile operating system ", Is just another Pants for android, lets say, Cyanogen without android ( Google's android), does not exists!!
It's not just "another pants for Android". You can flash it with entire Google framework completely ripped out... in fact that's the *only* way to install it, Google Apps are an optional package. Cyanogenmod includes many tweaks like Privacy Guard that Google will never bother to include while not deviating from stock Android in terms of UI and other features and IMO that's what makes it great. Stock Android can be stupid - I bought a Moto G for my mother and was extremely displeased to find out one can't even customize QuickSettings panel there. The option is just missing. Cyanogenmod is a perfect solution if you want full control over your device but don't want to mess with things a normal user doesn't really need.
Microsoft backing CM doesn't worry me because I hate MS (I don't - only some of their products *cough* Windows 8 *cough*). It worries me exactly because I *don't* want CM focusing on distancing itself from core Android. (And potentially disappearing once MS is done with it)