I attempted to configure seperate instance of log4j repository, but came across a message "console appender may be in a loop" type of message. As it turn's out, systemAdaptors exist that replace the system out and err streams. These adaptors themselves use the log4j framework to log messages. To get around this problem I exposed two operations on the log4jService JMX Bean "uninstallSystemAdaptors" and "installSystemAdaptors" as managed operations. Using these during DOMConfiguration.configure();
Is this a bad thing to do? It just means that no other way one can even create their own instance of log4j repository if they cannot switch the systemadaptors off temporarily.