R – sharepoint – deploy web service without creating a virtual directory

You can do what you want, and get WCF to read configuration from where-ever you like. I built this once, to allow each WCF service to read from its own config file. Good for testing and independent deployment. The technique involves overriding the ServiceHost.ApplyConfiguration method.

This blog post has some additional details and full source code.

Another approach of general interest might be to let the WCF service read its config from a centralized store somewhere - a database, a remote file server, etc. You could use the same basic CustomServiceHost, and just modify one method to load from a database, or whatever.

ps: the reason IIS is disappearing is, I suspect, you have an exception occurring in the WCF ServiceHost.

If using Visual Studio 2010 you can right-click on the project for the service, and select properties. Then select the Web tab. Under the Servers section you can configure the URL. There is also a button to create the virtual directory.