Hi,
as I wrote earlier, we face the same problems, but right now I'm working on a solution for us, where we will ship our EARs along with a CLI-Script. That way the admin will deploy the appication not by copying it into the server manually, but by executing the script (with some local modifications).
This script will then create all datasources, queues, topics and security domains ans so on and also deploy the archive into the running server. I think this will be acceptable and maybe also suitable for you?