Question about CI XSS filter and HTMLPurifier

You clearly don't properly understand XSS and SQL injections. They are separate things. What you are doing now is applying xss filter for both input and output, so you are escaping data twice - you are going to have a bad time if you do this. Instead, you should use xss filter on output and on input use CI's query builder and/or prepared statements.

because I can not use CI input validation with a WYSIWYG editor (Am I right?) so I use HTMLPurifier instead.

I don't see a reason why you can't use normal validation. WYSIWYG editor sends data as a normal form data.