Separation of Church and State

It is obvious that during the reign of the Tudors and Stuarts and others throughout this time period separation of Church and State was not in effect. Not really a hint of an idea really. It hit me sitting in class, how strange that would be. To have the person who advised me on my spiritual matters and personal beliefs also in charge of the raising and lowering of my taxes…what a strange world that would be. Granted, that would work if said ruler was perfect, equally just and merciful but taking a look at old Eddie, Lizzy, and Queen Mary herself…they are far from it. 
How would it feel to be under the rule of a religious leader that used their political power to sentence to death hundreds of people based on their religious views ("Mary Bloody Mary")? And then the next day show up to church and tell you that God in Heaven commands us to be good and keep the commandments. It's not difficult to see that someone as determinedly advocating freedom as Milton did would have some serious issues. Sometimes in the past people have been okay with this, for instance, the notion during the beginnings of the Roman Empire that nothing was so important as the perpetuation of the state of Rome.

The Pantheon in Rome, Italy

If obstacles arose any action was fair game as long as Rome came out on top. And everyone was just fine with it. One difference, I should mention, is that these people refused to be subjected to kings (instead they eventually vested this power to emperors that they all pretended didn't hold supreme power over them. Interesting tidbit: according to my Classical Traditions professor you could walk up to a Roman citizen when Caesar Augustus conducted the Roman Empire and he would declare that he was a free citizen in the republic of Rome. So crazy!) 
Anyway, I think it is more important to contemplate that while Milton is pushing more radical ideas (Eikonoklastes, accrediting regicide, reformation in general) his ultimate goal is to create a platform for freedom. Freedom from the arbitrary decisions of a corrupt and/or very hard-of-hearing monarch. 

Has not freedom been the cry of people for thousands and thousands of years? Milton is laying more bricks in effort to continue building the "pantheon" of freedom. 

Questions: Is it fair or plausible to boil Milton's arguments down to simply a cry for freedom? Do you think that Milton is at all suggesting a separation between church and state?