Totally agree. Just got eliminated during the 1st round during a terra mystica tournament because of a non playing participant. The remaining time does not make sense, because it depends on your position with respect to the defecting player: if they are in a different time zone especially, when they do play it can mess up the player playing before or after (depending on time).
But taking current score is a dumb way too, since at the beginning the differences are just random, or even worse with terra mystica, just the result of the initial bidding.
If the player is late early in the game (like after one day), they should be expelled and the game goes on.