Did you consider generating the wsdl from your endpoint, editing prefixes in it and then publishing the endpoint with the modified wsdl?
I'm not sure I'm getting you right. This is how it is currently developed. An endopoint interface annotated with jax-ws standard annotations. The wsdl is generated from them, however which annotation would you use to specify the namespace prefix for the web service? The package-info.java is the only way I found out I could use for this purpose but that didn´t worked.