The Sykes-Picot "Agreement" occurred because the Ottoman Empire had long proved an obstacle to Western imperialism in the region, and colonialist powers wanted to divide it into disparate countries that were almost guaranteed to cause conflict. Both Syria and Libya were destroyed within the last two decades because their governments were explicitly anti-imperialist. Historically, the Levant region has been unified while simultaneously containing multitudes of ethnicities, including Jewish communities that were largely treated better there than in Europe. The Shia/Sunni split largely only concerns Iran, which I don't think would join a unified Levant. The importance of the split itself is also largely overstated by western political theorists because the idea that the region is ungovernable and full of in-fighting is used as a causus belli for western imperialists.
Perhaps the modern people would not unify specifically to overthrow western imperialism (although given the massive negative impact of imperialism, I'm not so sure), but their unification would pose an obstacle to imperialism simply by making them stronger and less vulnerable.