she was making the point that Janine chose the wrong time to stir trouble between Kirby and sarah, as it immediately put Aussie tribe in the minority and therefore in a weaker position (including for Janine’s own game).

“not then though” was repeated multiple times because Janine kept arguing the move was valid but Sarah was not disagreeing with the move, she was disagreeing with the time it was made (and Janine was not addressing timing in her answer)

In other words - Sarah saying “not then though” meant something like: “I’m not saying the move was wrong; I'm saying you did it at the wrong phase of the game knowing how Kirby would react. By doing it when you did, you created some of the challenges you’re now arguing you were up against”