This is what I have in my site.xconf file. I think the key was excluding the com and wt classes, though I didn't get it working here. I include the ...stdout=false to keep logging messages out of the methodserver logs.
<property name="wt.manager.cmd.common.java.extra.args" overridable="true"<br"/> targetFile="codebase/wt.properties"
value="-javaagent:/software/ptc/wc10/Windchill/codebase/jrebel.jar -Drebel.packages_exclude=wt.,com. -Drebel.log.stdout=false"/>
Craig Raymond
Windchill / Web Developer
BAE Systems