What is hosting the WCF? Is it installed as a Windows service?
Is it on the client machine? If so, do other machines connect to it?
If
1. It is a windows service
2. It is on the client machine with the desktop app
3. No other machines connect to it
Then just add an licx file to the service .exe build with the licensing information you need.
http://www.atalasoft.com/KB/Article.aspx?id=10128