To be fair Microsoft had support documentation on how to disabled and remove GWX correctly and most of the third party tools were overly aggressive and did not follow the documented process. They were basically watchmen programs that looked for the GWX process and would force kill it. If you used a program such as Never10 that used the correct process you would have zero problems (Never10 is basically just a pretty UI that adds the two registry entries to instruct Windows to disable GWX).

I agree that MS will counterattack this tool though. Almost every time there is a Windows Update it restores all of the modifications these tools make. It was the same with the GWX killers that did not follow process. Unfortunately there is no process to disable telemetry (outside of Enterprise versions).