You are right in that aspect early islamic caliphates were totally secular, they didn't have the same experience as Christianity, heck even multiple religions were flourishing side by side something unheard of in christendome. There was a clear separation between the state where the amir handled worldy affairs using worldly wisdom and knowledge and the imams handled spiritual matters and stayed there. Other then the few times the khawarij rose up, things were pretty straight forward!!!The argument for secularism is confusing when you ignore the different cultural backgrounds.
By trying to fit europes experiences and culture into something quite different you will not understand whats going on.
The church was opposed to science and progress and had a stranglehold of the people and lands ,
the only way to progress was to destroy the churchs power and then relegate the role of religion into just private affairs.
Islam has no church and was never anti-science of progress, and there was never a clergy or organization.
So the arguments against secularism are meaningless,
we never had rule by priests, in a way most muslim states historically were secular.