I don't think there is any problem having several java versions installed on your system.
In order to Firefox to find the java version you want to use, there should be a symlink in the directory where you have Firefox installed that points to the libjavaplugin. If you want java 1.5.x to be used, you need to change the symlink.
Here is what is on my system. Your paths likely will be a little different.
Firefox on my machine is in a directory: /usr/firefox/firefox and the plugins directory where the symlink is - /usr/firefox/firefox/plugins. The symlink is called libjavaplugins_oji.so. This points to the java directroy.
My java install is at /usr/java/jre1.5.0_06. The real plugin is in path -
/usr/java/jre1.5.0_06/plugin/i386/ns7/libjavaplugin_oji.so
Keep in mind you need to enable java in Firefox.
So, have a look at the file in your Firefox plugins directory. Do a command 'file nameofthesymlink' and it should show you that it is a symlink, and where it points. Change the pointer to point to the java version you want to use.
Unless you have a need for the old java install, by some other application, deleting it should have no effect.
When I install a newer java version, I just install it using the installer from Sun, and make a new symlink. If you have never made a symlink, see the man page.
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