Please spare us the extremes of the governance model, it applies when it applies and it doesn't apply in all cases. It is a bit extreme to imply that al-Qaeda is pushing for "needed" change, or that religion has nothing to do with it.

Nonsense, if you change the government in most these countries and install what you believe to be legitimate government al-Qaeda will still exist and target that government for not embracing Sharia law, if you take religion away al-Qaeda can't exist. Furthermore, you can't separate governance and Islam, the religion dictates the form of governance one should apply.

In this case you're looking at the wrong forest. This isn't about good versus evil governance, or ineffective versus effective governance, both sides in these conflicts are led by tyrants. In the real world different interest groups compete, often violently, there are few cases in the Middle East and Africa with the current state boundaries that peace is possible without the state using what we would consider excessive coercive power. In time other political arrangements may be possible, but not in the near term.