It's about time they shut down these rogue deprecated client versions. This allows for a better consumer experience across platforms and enable Microsoft to develop new, innovative functionality and services.
Also, we all know Skype is widely used for terrorist communication. Consolidating the client base will surely streamline access for lawful interception, thus helping government agencies like FBI, CIA, NSA in protecting people's safety and freedom (US subjects', that is).
I don't see why they shouldn't? If any, VOIP is a threat to traditional cellular operator's business models of selling minutes for a premium. Microsoft and Apple on the other hand aren't particularly concerned about these business models. They are primarily hardware manufacturers and suppliers of additional internet-based services - yet they are not cellular operators or internet providers. As such, they need not be greatly concerned with voice calls. Furthermore, voice call functionality offers little to no potential for product differentation or as a unique selling proposition. No one bases his purchasing decision for or against a particular handheld device (iPhone, Lumia, etc.) or platform (iOS, WP8, Android) on the quality or functionality of voice calls (which both are limited and given by networks anyway).
Though maybe people like FaceTime's (or iMessage's, for that matter) ease of use and quality - which only creates a "vendor lock-in" for Apple's own platform - obviously good for Apple.
The competition between platforms is about software and app ecosystem. As such, I don't see why they shouldn't make a play for VOIP. All it needs is an internet connection - which can also be a cellular one.
They just have to be careful not to alienate carriers not so much to stop them from selling or supporting their devices on their networks.