I find it strange that I can install a flash blocker that allows me to whitelist certain websites but that similar functionality seems to be missing for Java... the easy answer is to not allow java to run unless the site or even specific URL is in a whitelist.
There is a Firefox feature request to add the ability to block all types of media (Flash, applets, other plugins) by site: bug 94035. It was created in 2001. More than 100 duplicate bugs have been added over the decade since. It's still not been implemented.