JMS is just another deployed service in JBoss - so just undeploy it (i.e. move the JMS directory out of you deploy directoy). Nothing uses it explicitly so you should be able to do this without a problem. That being said its probably not going to affect the performance of JBoss by removing it other than sprobably speeding un the startup time.
BTW: for future reference JBoss questions should really go in the JBoss forum.