That is by far the easiest thing to answer and the easiest to solve. It is also the only option that makes sense. Treat it like a match that has been abandoned and replay it. Start next season the same way that this season started. Easy.
On top of that, you build in any contingencies you need so if something happens again then the rules are in place to decide. As it is the clubs themselves are being left to decide what is best and obviously their current positions changes their thinking. It's effectively allowing people to decide who gets promoted/relegated instead of them doing it on merit.