Separation of Church and state is an excellent concept. The state has no business getting involved with the Church. But many people, ironically enjoying the fruits of Christian labor, believe it cuts both ways: The Church should have no influence on the state. One of the better arguments they use to sustain this claim is that a theocracy is bad for theists too, because the wrong kind of theist can be in charge.
Of course, this is 100% true. You don't even need to look at the dreadful history of the world to see this, there are a few Theocracies in the world to prove it. But the argument is also flawed in numerous ways, starting with the fact that there is no system of government that can fully solve the problem.
See, the first problem with the argument, particularly as it was phrased by the person who inspired this article, is that it confuses desire with need. This person gave the example of "Protestants" living under Catholic rule, or Evangelicals living under Mormon rule. But here's a question: What if they're right?
If Catholicism is true, I certainly wouldn't be happy (or likely even alive, I'd have been executed for heresy), but I would be wrong in my displeasure. If Catholicism is true, I should become Catholic, all governments should conform to the Catholic God, and all who sin against Him are criminals regardless of whether the law agrees. If Catholicism was true, a Catholic Theocracy would be "bad" for non-Catholics, but good overall.
But regardless of which religion is true, someone's religion is dominant. You can't solve the problem of one group of Theists being unhappy by making other groups of Theists unhappy. It would be like trying to please atheists by taking power from the aforementioned Catholics and handing it to the aforementioned Muslims. Religious morality, at its core, is a bunch of "thou shalts" and "thou shalt nots". Legislation, at its core, is a bunch of "thou shalts" and "thou shalt nots". Thou shalt pay thy taxes, thou shalt not drive more than 20mph in a school zone. In our society, the absence of a Theocracy does not stop one group of people imposing their morals on another. Instead, it makes it easier for the dominant class to impose their morals on each other.
Even Democracy does not solve this problem. Democracy, in its purest form, is mob rule. In a fair and just society, even the rights of the minorities are inalienable, but in a true Democracy, the will of the majority reigns supreme. In fact, ironically, a Democracy can be a Theocracy at the same time (as it will be in the Kingdom of Heaven, for God will win 100% of all votes). Here on Earth, if the majority agree with Theistic policies, those will be enforced. Indeed, the very reason this debate ever happens in a Democratic society is precisely because Theists are often popular enough to be threatening to Secularists.
But ultimately, even this may not be as much of a problem as Secularists make out. There may well be seriously intolerant religions out there which we don't want in power. I certainly wouldn't want to live under pure Islamic rule. But what about tolerant religions, like Christianity, from which opponents of Theocracies almost universally benefit? "We hold these truths to be self-evident, that all men are created equal, that they are endowed by their Creator with certain unalienable Rights, that among these are Life, Liberty and the pursuit of Happiness." These words, found in the U.S. Declaration of Independence, certainly did not come from a place of Atheism. We hold that all men are created equal, and are endowed by their Creator with certain inalienable rights.
Inalienable means not subject to governmental approval. All men, regardless of ethnic background, gender, age, sexuality, or even religion, were considered equal by the Theistic, mostly Christian founders of the United States of America. It is easy to consider the U.S., at least historically, to have been a Theocracy. A Theocracy which protects the rights of the unsaved.
Of course, the U.S. has never been a true Theocracy. Though governed with religious principles, the Founding Fathers did not even share, much less rule with a common religion. Nevertheless, denying their religious motivations would require the erasure of the religious language they used in the founding documents.
Of course, all of this applies to more than just the U.S. The effect Christianity, in particular, has had on the world is undeniable. Many freedoms, including the freedom to challenge the ruling class regardless of their religious affiliations, are new, and unique to Christian/post-Christian societies. Nevertheless, a true Theocracy is currently impossible, as it will always have to be carried out by human mediums. This is true even when they are acting on behalf of the true God.
One only has to read the Old Testament to see this. Though Israel genuinely did have word from God Himself, they failed miserably to enforce and obey His laws, even to the point of begging God to leave and send them kings instead. The result? Anything from complete anarchy to total tyranny. For as long as human beings have formed societies, there has never been a true Theocracy, and it is impossible for us, as non-gods, to ever set one up.
But a time is coming when Jesus will sit on the throne. Setting aside the 1,000 year reign on Earth, He will forever rule the Kingdom of Heaven, and even the Kingdom of Hell. True Theocracy. There is nothing Secularists can do to stop this. No amount of arguments, no amount of earthly laws, not even the sheer force of military might, will be able to stop Jesus from taking His rightful place as Lord. But as sinners, we are all guilty of treason.
There are two options. The first is to continue rebelling until He takes His throne by force. At this point, you will be condemned, and given due penalty for every sinful thought, word, and deed. Alternatively, you can make use of your grace period. Accept Him now, while forgiveness is available, and you will be given free citizenship in His everlasting Theocracy, which I can assure you, you will not be disappointed in.