Quoting from http://jolokia.idea.informer.com/proj/jolokia
Configuration is currently done via servlet init parameters, which need to be set in the war agent application's web.xml
Configuration could be externalized if other Servlet specification compatible means could be used.
Using ServletContext init parameters instead would enable to set the configuration in a separate file when deploying on Tomcat (application's context.xml) as an alternative to edit web.xml. Code changes necessary for that should be minimal, and there's no overhead.
A more heavyweight change, but with support for virtually all JEE/Servlet containers is using JNDI environment properties.
I personally focus on tomcat, so the first suggestion would be sufficient for me currently.