The problem with historical explanations for current events are all the intervening factors/events that took place since then. The further we move from the present, the harder it is to draw a clear link between cause and effect. Imperialism certainly created many problems, but Middle Easterners had a century to resolve them. Furthermore, they did a good job of creating numerous problems of their own.

The main problem with "artificial borders" is not that they're artificial per se but that no domestic group was able to enforce those borders upon the rest of the population. This lack of dominance and monopoly on the use of force allows for constant challenges to the regime's rule. Contrast the Saudis, who overwhelmed all domestic opponents, with the Iraqis, who did not. Both have problems with establishing a nationalism, both have significant minorities, but only Iraq keeps on erupting in violence on a regular basis.

I should also note that just like partition doesn't end conflict (but rather moves it from the intra-state level to the inter-state), having homogeneous (in terms of religion) states in the Middle East would shift warfare from the domestic arena to the international one.