Im not 100% sure on the details but to my understanding when you paused after the 128 from fally got gassed there were still more than 128 in the GDZ zone alive. Obviously the pause got abused to take out all high levels from the smaller clans who could have also won, so if you just take the last 128 remaining after the pause that would be unfair.
I think you should probably manually check the remaining players and remove low level bolt raggers and put all high levels with good gear into the 1v1s.
Otherwise you pretty much just hand money to the same clan that already benefited from the bug/pause again.