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You can create custom signatures to block/log file/folder access/changes.
This can help you in monitoring the changes.
But incase you Block the c:\windows folder from any changes then you might run into issues when hotfix/patch/servicepack install happens.
So test thoroughly.
This client is investigating a few options, including some which will affect their patch management processes. This may not be the optimal solution, but it does provide them with one alternative.