Comment 16 for bug 288397

Screw update-alternatives. This didn't work either. It doesn't even change the symlinks in /etc/alternatives/ . And I also didn't even had the /usr/lib/xulrunner/libjavaplugin.so and /usr/lib/mozilla/plugins/libjavaplugin.so files. I ended up creating every symlink manually:

sudo ln -s /usr/lib/jvm/java-6-sun/jre/lib/i386/libnpjp2.so /etc/alternatives/xulrunner-1.9-javaplugin.so
sudo ln -s /usr/lib/jvm/java-6-sun/jre/lib/i386/libnpjp2.so /etc/alternatives/xulrunner-javaplugin.so
sudo ln -s /usr/lib/jvm/java-6-sun/jre/lib/i386/libnpjp2.so /etc/alternatives/firefox-javaplugin.so
sudo ln -s /usr/lib/jvm/java-6-sun/jre/lib/i386/libnpjp2.so /etc/alternatives/mozilla-javaplugin.so

sudo ln -s /etc/alternatives/xulrunner-1.9-javaplugin.so /usr/lib/xulrunner-1.9.0.4/plugins/libjavaplugin.so
sudo ln -s /etc/alternatives/xulrunner-javaplugin.so /usr/lib/xulrunner/libjavaplugin.so
sudo ln -s /etc/alternatives/firefox-javaplugin.so /usr/lib/firefox/plugins/libjavaplugin.so
sudo ln -s /etc/alternatives/mozilla-javaplugin.so /usr/lib/mozilla/plugins/libjavaplugin.so

If any of these files already exist they should be deleted, otherwise the new symlink cannot be created.
I made a shell script to do all this. I'm attaching it. Don't worry if you get an error message saying that something can't be deleted.

This works 100%! I tested it on two computers and this workaround also survives a reboot.