Ok so I wrote to the JBoss developers directly to get an answer to this and this was their response:
modelmbean persistence is available in jboss 4 (cvs head). no one has tried to make a significant part of the server configuration persist in this way: the first step is to make all the server mbeans into xmbeans.
The model mbean persistence might get into 3.2 (it might already have been ported, I'm not sure) but is unlikely to get into 3.0
Matt Munz implemented it. If you search to dev list for his posts you can find the discussion of this feature.
I am sorry to disappoint you, but this question still stands. I did not have any time to implement persistence of mbean attributes the way I see it (moreover, it was mentioned that something similar would be present in JBoss 3.2). I still consider this issue to be VERY
important and will inevitable have it implemented. I can let you know then, or may be we can do it together :-)
So what I am now doing as a workaround is making a copy of my service.xml file in the conf directory. In order to save my MBean runtime changes, I modify this file manually from code (using DOM) and copy it to the deploy directory on server restart. This way my mbean changes persist, and JBoss doesn't undeploy and redeploy my mbean every time I change its service.xml file.