Sources? Not sure it changes anything even if she did. She obviously didn't get the special dispensation with regards to her duties. That coupled with the fact that apparently KY and the Feds both believe that marriage licenses issued by her aides in her absence are perfectly valid. She could have stepped back and let the office continue to operate the way it always had, yet she chose to grandstand. It is my understanding that she was cool with her aides issuing licenses before this whole fiasco, I may have heard it on NPR and cannot find a relevant source at the moment.
Numbering the questions in red and responding accordingly.
1. She's not a federal employee, but yeah, if you work for the government and you don't follow the law you should be punished according the the existing laws. If that includes jail, then so be it.
2. If they don't do their job, then it is up to the existing work place laws for removing that person from their job. She was a special case, as they couldn't stop people being disenfranchised from getting their marriage license while at the same time wait for the bureaucratic process necessary to remove an elected official. Had this been one of her aides instead of her, they would have simply been fired.
3. I am not sure I follow your question. Are you asking if a Judge should be able to get gay married if they are about to determine if its legal?