I'm assuming that the rule is in place, like any other situation where a card carries over, to prevent players from feeling like they can play wreckless during the last game of a round.
I think they could adjust the rule and suspend a player for a wreckless challenge after the fact. The downside of the rule is, if Altidore gets a second yellow he is out. The first was kind of soft, IMO.
I think you play the regulars until the second half. Take out Altidore, because of the yellow, as well as Bradley and Onyewu, two players who have moments of carelessness which leads to silly cards.