I think that I would need to be an expert in Middle Eastern politics to fully grasp the essay, but I think that the author makes it reasonably clear that Middle Eastern conflicts are made worse by the 'US' and 'THEM' mentality of Sectarianism. Unfortunately, the Sectarian divides seem to be so complex and so convoluted that few people can make sense of them, least of all outsiders. For this reason, outsiders (like the US Forces) should always stay out of Middle Eastern conflicts when possible and just let them run their course for fear of the exacerbating the problem.
The conclusion of the author is good as it promotes the obvious idea of side-stepping religion to build non-sectarian national institutions.
In my next article on this topic, I will discuss how we got here, the crisis of Sunni identity that sits at the heart of these conflicts, and how Western and, in particular, American policy should change to accommodate the realities of the Middle East and to focus on building and reinforcing non-sectarian national institutions and national forces.
However, there is a problem to the authors goal - the Islamic system is not geared to allow the separation of national institutions from religious ideology. In fact, the system of Islam is directly opposed to this simple ideal. At every available opportunity the Islamic system will seek to shape civil and criminal law in its own image. Politicians who oppose the Islamic system will lose political power, and politicians who collude with the Islamic system will gain political power.
So it's all very well to 'focus on building and reinforcing non-sectarian national institutions and national forces', but this can only really happen if the Islamic system is first drained of its power. The simplest and best way of doing this is to fund and promote Science in all its forms, and complain bitterly when atheists, agnostics, and apostates are locked-up or threatened. It's not a quick strategy, but grass-root strategies never are.