The other problem with focusing too much on the prospect of an Al Qaeda ascension is that the costs of inaction in Syria are woefully underrepresented in the policy debate. Even if the rebels ultimately prevail, if the US continues to sit on the sidelines as the human toll rises, it could face a decidedly anti-American government in Damascus whether jihadists come to power or not.
For the Assad regime, Al Qaeda’s presence in Syria not only serves to fend off external threats (like US intervention), it reduces one of Assad’s many internal threats: the defection of Syrian minorities to the rebels' side. Jihadists consider the minority Alawites (who dominate the Assad regime) and Druze (whose support is being sought both by Assad and the opposition) to be heretics, subject to the punishment of death. The historic animosity between these groups and Syrian Sunnis is probably enough on its own to keep them loyal to Assad. But a jihadist death-sentence goes a long way toward squelching any remaining doubts.
After witnessing how Christians fared against Al Qaeda in Iraq, Syria’s Christian community is not giving the rebels the benefit of the doubt, and instead is operating as though a rebel victory means that Muslim extremists – or at minimum, a decidedly anti-minority government – will come to power. Most remain with Assad for now, but the more that the rebellion takes on an Islamist hue, the less likely those Syrian minorities will turn on Assad.
Of course, the prospect of Al Qaeda or other extremists coming to power, or having influence on a post-Assad regime would also be a nightmare for US regional interests. So that scenario should be factored into policy calculations, even if it is unlikely at this time. Yet the amount of attention that this scenario is receiving, especially in US intelligence circles, suggests that the magnitude of its effect on policy formation may be disproportionate to its likelihood.