Something about what you have stated seems like it might be key to what you are experiencing. You say that you ran the tool, then had the problem. From your experience you knew to revert the site to a backed up copy, but this did not work for you. This tells me that it is not what Security Assist is doing to the page that is the problem since you can revert to the previous versions of these pages and still have the same result.
What exactly is the result that you are getting when you try to access one of these pages? Is it a server error or a 405 type of restriction? Please post back and include any details that you can about the error.
Also, if you could post back with a sample site folder in a zip archive that you are having this problem with it might help to determine what the problem is. What is the web server you are working with?