you mean in application server? Yes...you must package your aspects/xml in a .aop package. See reference manual and tutorial for more detail.
You are correct about the problems you will encounter. JBoss AOP does not currently re-weave (or weave) already loaded classes. We're currently researching the possibility of using the Hot Swap feature of java.lang.instrument, but til then, you'll have to do some of the tricks you suggest to yourself :)