Long before I knew anything - not that I know much even now - I desgined a web app in php which inserted data in my mysql database after running the values through htmlent
I had the exact same problem. Since I had multiple clients running the application in production, I wanted to avoid running a PHP script to clean the database for every one of them.
I came up with a solution that is far from perfect, but does the job painlessly.
Change your "display data as HTML" method to something like this :
return html_entity_decode(htmlentities($chaine, ENT_NOQUOTES), ENT_NOQUOTES);
The undo-redo process is kind of ridiculous, but it does the job. And your database will slowly clean itself everytime users update the incorrect data.