I cant seem to find a way to undeploy or turn off an application whilst JETTY is running. Is the only way to kill JETTY and all other apps running?
You can do that in a few ways.
If you have the deploy module enabled, just move the {appname}.war (or {appname}.xml) out of your ${jetty.base}/webapps/ directory, that will undeploy that webapp.
deploy
{appname}.war
{appname}.xml
${jetty.base}/webapps/
Another choice is to have JMX enabled and just .stop() the webapp in question.
.stop()