In context of current version. I was thinking of an additional (leftmost) column of checkboxes labelled Disable/Enable in S&R and Mark settings. I can't see how that would be any harder to use than the existing columns of check boxes.
Then, when the rule set was applied to a document the Disabled rules would be ignored, i.e. there would be no user interaction for those items, because, virtually, they don't exist
BR