Although the author of that article tries to make it seem like this is near unstoppable, there are actually several feasable methods by which this can be stopped. 2 off the top of my head.
Install an IPS. An IPS can do a deep inspection of the packet no matter the port and identify/block unwanted traffic.
When Skype servers are used as a form of proxy there are several options. A)Have the firewalls block Skype IP addresses. B) Decrease the timeout value for UDP packets on the firewall.