You don't need to remove it from your environment, but you may want to edit the run.sh for JBoss and clear the classpath at the start of the script. The run.sh sets up the JBoss classpath for required libraries during the course of the script. Newcomers have found that the classpath inherited from the UNIX/Linux environment can sometimes cause JBoss to fail on start up - mainly because the libraries override those used in JBoss.
OF course, your other option is to clear your classpath in the environment. It depends on your requirements for running other Java programs besides JBoss.
As always, YMMV.