Unfortunately Windows Installer (which Java uses) doesn’t have an API to uninstall program manually. Attempting to manually remove it from ‘Add Or Remove Programs’ tend to cause more problems than it solves, so, until we can figure out a work around you will need to run the uninstallers from the commandline first.
/REMOVEOLD may leave two versions of the JRE if you’re using both ‘JRE 6 update 31’ and ‘JRE 7 update 3’