I have a question that one of my clients raised. We have a CSS editor that we use locally and it;s loads the HTML Purifier script as a filter. We only load the program as a filter on the CSS editor page and that's it. We do it as an include followed by passing the form data through following the example list here as step 6: http://htmlpurifier.org/live/INSTALL
The question that got raised was to just load the filter as an actual wp filter and "keep it loaded" in the software. Now this is the only place that it would get used so I have to admit that I'm against that. Unless of course I'm going to run all of the content through the filter along with the kses filter. We only run the filter once currently before the data gets saved. We don;t run it again when the code is added to the output since it;s already passed through.