1. Closed source apps are not the threat (Nowhere does it say that the dialer, home screen, messaging app, or camera are a part of the OS. All are replaceable, and all replacements integrate just as well as the original, it's not an iPhone).
2. Google controlled Android through legal means - If you want to make your Android phone in a factory, or if you want to use any google app, you need to obey their rules. So if yo want Play store, you have to play along.
3. Cyanogen saw Google as a threat, but Google didn't see Cyanogen as a threat. Cyanogen didn't die because of Google's behavior. They died because of terrible execution.
Remember the spat over split-windows. Google didn't ban the appstore (despite being able to), they demanded that the environment not be _too_ modified.
Cyanogenmod backed down and Google let it go.
The only thing is that they were forbidden to _package_ it, but opengapps is still around.
4. Google isn't closing-source because of Cyanogenmod or other custom Roms. It's bigger threat is Samsung or Amazon.