I like your analysis and your view of the bureaucracy versus the laypersons; I would not argue against most of what you said.
I think most of the ills have come when these institutions feel like they are losing some of the power they either had in actuality or perception: the reformation and the counter-reformation were terribly bloody; the return of Catholicism to the English throne after Henry VIII's death sparked decades of brutal violence throughout the UK; the entire back and forth of the French Revolution; etc., etc.
One reason why I think that Islam is not the all-violent religion that some assess it as. Islam has been losing power across the Middle East over the past sixty years (precisely when a lot of Muslims felt Islam would gain power due to the end of colonialism). As with other institutions, religious and political, many radical Muslims have reacted with violence.
I see that in the history of Christian and Western institutions and nothing I have seen convinces me that it would not happen again if Christians and Western governments strongly perceived a transfer of power from their institutions to foreign institutions.
