I think the headline implies multiple interpretations, certainly it suits the taste of sophisticated readers of New York Times. Yet I wondered, is "do in sb. or sth." a common phrasal verb in daily communication, meaning " to ruin, murder or destroy completely"?
Let's take a look of how other news outlets chose to write their headline.
Netherlands THRASHES Spain 5-1 in World Cup opener - SFGate
Netherlands THUMP Spain in Salvador - CNN International
Netherlands DISMANTLE Spain at its own game - USA TODAY
Netherlands TROUNCE Spain 5-1 - CBSSports.com
Scoring Onslaught Does In Defending Champions - New York Times
= Scoring onslaught (launched by Netherlanders) Does in ( to bring about the defeat or destruction of ) Defending Champions (Spaniards who are defending the World and Europe Championship titles.)
It also implies that it's far too early to tell how this crushing onslaught will finally turn out for Spain in defending its Championship, given that the Spaniards also lost their opening match to Switzerland in the group stage in South Africa four years ago.