At this point, I think the best thing to do is to keep the status quo for this season. That means only rookies in the draft, and waiver priority is re-set next year, with the best team getting #1. That way, nobody can complain that the rules were changed in mid-stream. It's the fairest solution.
For *next* season, I vote that the waiver priority carries over, and that all players be draft eligible that aren't on a roster.