Hi Paul,
first of all, I moved this discussion to the development section of the forum.
Now, I see some alternatives for you to achieve what you need:
1) The user is supposed to specify handlers either using JAXWS annotation (@HandlerChain) or through the jbossws endpoint configurations (@EndpointConfig and then provide a configuration file with handlers specification in the deployment or reference a configuration in the AS7 domain). So the first option is asking users to properly annotate endpoint classes, not sure this is acceptable for your use case.
2) You could make sure a webservices.xml descriptor (JSR-109) is added to the deployment and specify the handlers in there. The descriptor is parsed during the Phase.PARSE in AS7.
3) You could also hook in a little bit later then what you'd do for 2) and modify the jbossws spi metadata that are created after parsing the webservices.xml descriptor. To be honest, you'd need actually create them most of the time, given it's not that common to have webservices.xml for JAXWS deployments. Btw, there's a little bug I just discovered here, I'm going to fix it later today or tomorrow.
4) Another alternative is using the Apache CXF API, but that would bind you to implementation details of cxf and still require some changes in jbossws for you to hook into the proper point in the endpoint publish process.. so not really a good option.