The killing of a leading Syrian opposition commander at the hands of al-Qaida affiliated rebels will add to the difficulties faced by western leaders over their policy for the country.

Kamal Hamami, of the Free Syrian Army's supreme military council, was apparently ambushed by members of the Islamic State of Iraq and the Levant following a meeting with them "to discuss battle plans".

Meanwhile, the Washington Post sharply criticised President Obama for dithering; but it is hard to see what effective tools of action the US and the west actually possess. The Syrian crisis is transforming the entire Arab Mashriq, encompassing Syria, Iraq, Lebanon, Jordan and potentially Israel/Palestine into one vast arena for what is now a sectarian conflict between Sunni and Shia Islam. Any external intervention bears the risk of an open-ended engagement.

What is happening in Syria today is not only a case of unparalleled regime brutality, it is a war in which the opposition has matched the regime with a violence that is as unconstrained as it is stained with sectarian sentiment. Lost in the much-quoted figure of 100,000 attested deaths is that, according to the latest data released by the pro-opposition Syrian Human Rights Observatory, the regime's share of causalities has been more than twice those of its armed opponents; some 42,000 dead as opposed to 18,000 dead rebels, and some 36,000 civilians (a figure which also presumably includes Alawites and unarmed regime supporters).

Those who hope that arming the opposition will help stem the regime's current resurgence and compel it to negotiate are making a dangerous assumption. Whatever firepower may be provided to the rebels will be more than matched by the regime's allies. SAM missiles may affect the regime's freedom in the skies, but it has sufficient alternative firepower in terms of its massed artillery and armoured forces to maintain its edge. Anti-tank weapons are of limited use in what is essentially an urban war. Unless there is truly massive external military intervention (which seems unlikely), the net result of seeking to manipulate the current balance of power will be to prolong rather than curtail the war. The history of the region shows that almost any outside interference (even on the part of neighbours) tends to end in tears. And the west, despite its long experience in the Middle East, remains profoundly alien to the region's most deep-rooted forces of religion, sect, ethnicity, tribe and clan, and seemingly incapable of grasping their complexity.

The killing of the FSA commander and a series of other similar recent clashes point to yet another layer of conflict that is only likely to be exacerbated as the war goes on. Arming one side of the opposition will lead to a struggle over access to these weapons and thus a weakening of the anti-Assad front, rather than the opposite. More significantly, however, it also suggests that the regime and its allies on the one hand, and the west and the FSA on the other, may end up in the same trench against al-Qaida and its affiliates. This may itself provide common ground for a political resolution, as elements of the regime have been suggesting for some time.

The real question facing the west and its allies today is how to deal with a future Syria that is more likely to have Assad at its helm – even if only nominally – than not. A subsidiary question has to do with what this entails in terms of realignment both with elements within the opposition and the forces supporting the regime. A prudent western policy would recognise and build on the seemingly paradoxical reality that the regime and Hezbollah have now placed themselves on the cutting edge of the war against terror, that Iran must be included in any political settlement, and that Russia is more than likely to compensate the regime for any erosion of its military power.

Its worst option is to stumble into taking sides in a historic and lamentable conflict and to be perceived to be biased towards one branch of Islam against the other. It may be worth remembering that this is not a region where historical grudges fade over time.