You are wrong, this is sensationalist journalism at it's worst. I run my own telecommunications business and I was very disappointed reading this article.
The patent makes absolutely no mention of 'eavesdropping' or intrusion by external agencies. You also specifically state that the patent makes no mention of this tool being hidden.
Further, your own summary of the patent request specifically states that it is for 'recording' calls, and even goes so far as to describe the application for integration into a router / call centre / business environment.
The point of this patent is call recording which is a standard business function for businesses who may need to record internal or external conversations for legal, training, or quality assurance reasons.
This is NOT illegal if participants are informed - it is a very widely used practise and is there to protect consumers as much as businesses.
This technology is already widely used for standard analogue and digital telephony, which is why you may often hear "Calls may be recorded for training and quality purposes" when you call your electricity provider, for instance.
Microsoft is simply looking at ways of bringing this concept to a VOIP platform, which will surely be a big asset for them in the Unified Communications space in business/enterprise.
You have to imagine all the businesses that are currently using Microsoft Exchange, which may or may not have integration with their telecommunications platform via Outlook. You even mention a software deployment as part of the 'call server' on the network (normally referred to as a Unified Communications Server).
Now, imagine if Microsoft were able to leverage their Skype aquisition and patents like this to deploy an enterprise-ready VOIP solution as part of (or as an addition to) future versions of Exchange.
Now you're on the right page.