I suppose it would be better than what is currently in place.
The one remaining question is how does it handle it in the event of a real desync. It obviously can't "wait for opponent" forever, and you've shortcircuited the timer.
Personally I think it would be better to do the waiting at the front of the timer instead of at the end.
So, you end your turn, and your timer does not start yet. Your opponent begins his turn, and the first action that occurs is to respond with an ack to the first player, letting him know the turn has begun. The first player's yellow timer starts when the ack is received. This way, you can still time out normally after 60 seconds, regardless of what the other player does, and the activation of your yellow timer is proof that the other person's turn has been acknowledged by the server to have connected and begun. It also ensures that the player who's turn it is has the earlier starting timer. It's the same process as now, with an ack required to start your initial timer. The benefit being that you can demonstrate in a screenshot whose fault the desync was, while keeping to the real 60 sec timer.
That's all you really need in a desync for event purposes, the ability to point out who caused the desync.