Comes Great Responsibility, as noted Political Theorist Ben Parker asserted in his conversation with Peter Parker. This is relevant today as it always, and especially in Afghanistan. The NY Times piece indicates that the administration pushed Karzai very hard and from many angles to get him to respect the election commission's decision.
There is a delicate balance here, as making Karzai seem like a US stooge would be bad for him, for the US and for Afghanistan. But Karzai's instincts do not seem to run towards institutionalizing the rule of law and other such behavior that is necessary for COIN success. So, careful persuasion is required: Senator Kerry, not Holbrooke; Gates and Jones calling the Afghan Defense Minister and making it clear that American reinforcements are dependent on this decision, etc.
So, what happens next? My guess is that Karzai wins the runoff with less obvious fraud, that there is no coalition, and that Obama goes ahead and provides McChrystal with much of what he asked for, but perhaps not all of it. But it is just a guess.