Even as the debate about arming the rebels took on a new urgency, Mr. Obama rarely voiced strong opinions during senior staff meetings. But current and former officials said his body language was telling: he often appeared impatient or disengaged while listening to the debate, sometimes scrolling through messages on his BlackBerry or slouching and chewing gum.

In private conversations with aides, Mr. Obama described Syria as one of those hellish problems every president faces, where the risks are endless and all the options are bad. Those views would then be reflected in larger groups by Tom Donilon, the national security adviser, and Mr. McDonough…

Mr. McDonough, who had perhaps the closest ties to Mr. Obama, remained skeptical. He questioned how much it was in America’s interest to tamp down the violence in Syria. Accompanying a group of senior lawmakers on a day trip to the Guantánamo Bay naval base in early June, Mr. McDonough argued that the status quo in Syria could keep Iran pinned down for years. In later discussions, he also suggested that a fight in Syria between Hezbollah and Al Qaeda would work to America’s advantage, according to Congressional officials.