Yeah... I don't really understand what their issue is to be honest. It really is up to Skype if they want to release their protocol. You can't really force anyone into being open source. I actually disagree with their methods, its the same as a closed source company violating the GPL when they steal source code like this.
Reverse engineering has given us so many good things - Samba, OpenOffice, Wine, MAME (and other emulators) the bitkeeper debacle, which gave us git. Then there are all the Linux and UNIX drivers that were written by reverse engineering windows drivers because vendors weren't supporting those operating systems.
The guys who reverse engineered Exchange Server were acquired by Cisco.
I don't understand why the Skype case is 'evil'. distributing the binaries may violate terms of service, but it isn't illegal in large parts of the world.