Hi Chris,
I think we are out of luck here so far. Both Rad Editor (phasing out) and CKEditor (coming in) have those issues. They have some markup cleaning tool on the toolbar but can only do so much.
I think at this point it is about educating clients on "what if this happens... then do that....".
I don't use the editor either most of the time. I just get the HTML from outside and paste it in. No patience to deal with them.
Sorry, I know this is not super useful.
Aders