"Action" has been deprecated and instead you should be using "ForceCreateOnInstall" and/or "ForceDeleteOnUninstall" instead.
You can also use "NeverOverwrite" on the component to make sure that the registry value isn't removed.
To set the value you can use a custom action that is scheduled to run only during the uninstall. Use NOT UPGRADINGPRODUCTCODE as the conditional for your custom action to ensure it only executes during uninstall.
For the custom action under Product AND Package add
<InstallExecuteSequence>
<Custom Action="YourCustomAction" After="InstallInitialize"><![CDATA[(NOT UPGRADINGPRODUCTCODE)]]></Custom>
</InstallExecuteSequence>