I'm certain AFC would rather have 6 points less or one round less of the FA Cup than have to face MK.
Im sure they would like one less round in the cup too.....very much doubt they would happily start a season on -6pts though.
Relegated, or miss out on promotion, all because they had to play MK Dons. You think MK Dons would give two fucks....they would laugh in their faces and make it even worse. The only club suffering would be AFC.
It would be an absolutely pathetic decision IMO.