Stripping CR and LF on save.

We upgraded from FCKeditor to CKeditor.. and now are seeing CR and LF being saved out in our SQL database. I found info on how to strip out CR and LF using the setRules function for tags.. However, this also strips the formatting when you shift to source view.  I just want to have the same behaviour as FCK.  When it saves, it doesn't pass the CR or LF, but shows html source properly formatted.  Is there some way to do this? Some sort of post-processor? or Am I going to have to go in every single place I used the editor and strip these out myself using some sort of regex?