You can use the FME Server REST API to publish workspaces, there's an example under the heading "Publishing a workspace to a repository" here:http://playground.fmeserver.com/using-the-rest-api/workspaces/
You can use either the HTTPCaller or a Python script to access the API.
(If you go the Python route, I'd heartily recommend using therequests module, it is amazing for working with REST interfaces)