How to execute a Custom Action as System user with Wix 3.0, before checking to see if files are in use

So I have a Wix 3.0 project that installs an IIS7 Native Code Module. When uninstalling I would like to be able to shut down the IIS7 application pools before deleting the file so that a reboot is not necessary.

I am using the appcmd utility to shut down the app pools in a CustomAction element, but when I attempt to do an uninstall I get this error before the customaction is ever invoked:

The setup must update files or
services that cannot be updated while
the system is running. If you choose
to continue, a reboot will be required
to complete the setup.

I have the "After='InstallInitialize'" property set on the CustomAction, because the documentation says that any deferred/not-impersonated custom action must come between InstallInitialize and InstallFinalize.

So is there some way to have a custom action execute before this check for files in use is made? Or disable this check for a given file, or make the check happen later in the sequence?