(1) Much is being made in the media about the "rift" between the White House and the Departments of State and Defense and the CIA regarding arming Syrian rebels. There no doubt were strongly held views on both sides of this matter, but this difference of opinion isn't some dramatic breakdown in the Obama Administration's foreign policy apparatus; rather, it's the result of the typical Executive Branch decision making process.
(2) The National Security Council, which is part of the Executive Office of the President, drives decision making on major "interagency" issues like this (and many smaller issues that don't rise to the level of public awareness and that don't necessarily implicate "security"). The NSC acts with the President's imprimatur, and their jurisdiction is incredibly broad. This does not change from one administration to the next. The NSC undoubtedly coordinated and drove this issue, presented all sides of the argument to the President, and the President made a decision.
(3) What's often characterized as a "rift" for sensationalist media purposes usually represents a legitimate difference of opinion on policy. Disagreement is healthy in any decision making process inside any organization as long as it doesn't turn personal, and the government is no exception. The American people unfortunately never see the long and passionate debates inside the corridors of power in Washington. The public is never well served by a policy choice that's made without a dissenting voice. Whatever your view on Syria and contrary to what the media suggests, this "rift" is government working as it should, rather than a sign of dysfunction.