Skype is a special case because the very nature of the Skype protocol is to effectively circumvent firewall blocks. Skype searches a way to connect to it's services by using different protocols/ports. So there is no simple way to toggle off skype without limiting also other services.
However, there is 1 possibility to block it:

1. enable the outgoing firewall and allow only the ports you really need, so skype cannot use it's normal ports to access its services and will tunnel through HTTPS instead.
2. enable the http proxy in transparent mode, so skype need to use the proxy.
3. block url's containing ip addresses instead of hostnames (example: http://10.1.1.1/test)
   

The last step is not implemented within the GUI of Endian firewall. You can configure it manually doing this:

1. edit /var/efw/proxy/custom-acl.conf using
   
   nano /var/efw/proxy/custom-acl.conf
   
2. add the following:
   
   ----------------------- snip ----------------------------------
   acl numeric_IPs url_regex ^[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+
   http_access deny CONNECT numeric_IPs all
   ----------------------- snip ----------------------------------
   
   
3. restart the http proxy
   

From now on you cannot connect anymore to url's containing ip addresses. But this is the only way to effectively block skype.