If you are using jboss 3.x, you remove all the services that you do not need from the /deploy directory.
So it otherwords, remove everything except jbossmq*.xml files.
How about using JBOSSMQ with another app server (such as RESIN, etc.)?
JBossMQ is based on JMX therefore any application server you are going to use JBossMQ with needs to have a JMX MBeanServer running. Also you have to make sure that the JBossMQ services are started properly (JBoss MBean lifecycle means: register -> create -> start -> stop -> destroy -> unregister).
Beside the integration with Message Driven Beans (which are application server specific) JBossMQ should run fine.
Have fun - Andy