It would make sense to me to do it as follows:

• Whatever lap the red flag comes out on, ignore the positions of that lap unless the rider has crossed the line and finished the race before the red flag came out. If you've finished the race, those results stand.
  
• Only those still riding on the lap when the red flag came out are eligible for a result (that means MD, GJ, etc, couldn't be classed as finishers)
  
• Either work out which of the transponders on the course was the one that everybody in the race last passed, and then work out positions from that, or:
  
• Use the positions of the competitors as they stood when they last crossed the line.
  

It's not a perfect solution as there will always be winners/losers, however it's about the only way I can think of where you have a fixed point that all remaining riders have passed and thus you can work out their relative positions.

Although I'm sure the FIM have a better solution than my simple brain can come up with