In the CIA's defense, you use the networks that are in place rather than trying to create your own conduits for arms. It's cheaper, and more reliable to tap into the Muslim Brotherhood's arms smuggling operation than starting from scratch.

I just hope that our spooks are not asking the Muslim Brotherhood which rebel groups aren't extremist Islamists.

New York Times:

The weapons, including automatic rifles, rocket-propelled grenades, ammunition and some antitank weapons, are being funneled mostly across the Turkish border by way of a shadowy network of intermediaries including Syria's Muslim Brotherhood and paid for by Turkey, Saudi Arabia and Qatar, the officials said.

The C.I.A. officers have been in southern Turkey for several weeks, in part to help keep weapons out of the hands of fighters allied with Al Qaeda or other terrorist groups, one senior American official said. The Obama administration has said it is not providing arms to the rebels, but it has also acknowledged that Syria's neighbors would do so.

The clandestine intelligence-gathering effort is the most detailed known instance of the limited American support for the military campaign against the Syrian government. It is also part of Washington's attempt to increase the pressure on President Bashar al-Assad of Syria, who has recently escalated his government's deadly crackdown on civilians and the militias battling his rule. With Russia blocking more aggressive steps against the Assad government, the United States and its allies have instead turned to diplomacy and aiding allied efforts to arm the rebels to force Mr. Assad from power.

By helping to vet rebel groups, American intelligence operatives in Turkey hope to learn more about a growing, changing opposition network inside of Syria and to establish new ties. "C.I.A. officers are there and they are trying to make new sources and recruit people," said one Arab intelligence official who is briefed regularly by American counterparts.

The civilian opposition - the Syrian National Council - is about 70% Muslim Brotherhood, which is why a lot of secular-oriented Syrians have either refused to join, or resigned in disgust. There's no need to wonder where these arms are going to end up; one way or another, the Brotherhood will probably control any post-Assad Syria and thus, any arms given to rebel forces will likely end up in their hands.