Are you not part of reality? If you are, then movement of your arm is an activity wrought by the conscious mind. I'm not trying to show you something unexplainable, I agree, it IS explanable. I'm simply asserting that the REAL movement of your arm is made to do so by a conscious mind, ergo the mind isn't simply passive, but also active. It is conceivable further, that the conscious mind is also capable of say, telepathy. This may be considered a greater form of affection on reality. How is it performed? Another matter, the fact is that once one is aware enough for it, then it may be done (for example). I'm not saying that sheer force of will will alter the reality around you. Of course not, first you must know how to do so. If it happens that we discover a way for the human mind to alter it's body's own gravitational field, then at that time such things as human flight may be possible. I'm not saying that the impossible can be done. I'm simply asserting that the human mind, a conscious mind, may have active affect on reality, as far as it's able. Right now, it would seem that the extent of it's ability to so is simply to move the body, and, through it, shape the world as it is able.
I would agree that you are in control of your mind (if not maximally), body (if not maximally), destiny(if not maximally), decisions, spirit (if not maximally), etc... Why do I say not maximally? Well, take your mind, for instance, do you have full use and control of your mind? Or just your thoughts? Do you ever daydream? How about your unconscious mind. I am not trying to say that you aren't in control of your mind... simply that you don't have full, or maximal control. Again, with your body. Can you make your heart stop on comman? How about accelerated healing? Perhaps you can control fat intake? or when you have to use the bathroom? I'm not saying you don't have control over your body. I'm simply asserting that your conrtol isn't full, or maximal. Destiny, and spirit. Do not other have influence in your experience? Perhaps the laws of a country influence your decisions, and so have perhaps a slight say in your destiny. I'm not saying you aren't in control, just that that control isn't maximal.
I accept and agree with the control you have in your life, as well as the control I have in my life. God doesn't control me, nor has governance over me. Part of divinity, or Image of God, is free will. Most theists would agree that we control our lives, that we govern our lives. If God has any governance in a person's life, it is a governance that is asked for and desired, ergo, free will is still intact, since the desired governance is not a contradiction of it. I exist, the universe exists. Existence is an axiom, I agree.
As for those actions of the Church members in the Dark Ages, all Christians can do is but apologize for them. The Catholic Church recognizes that it is simply a religious institution, and does not have any kind of final say in what science affirms as truth, nor history, nor philosophy. As a religious institution, the Catholic Church simply claims authority on faith and morals. This isn't to say that members of the Catholic Church can't break moral laws. We're human. As for Murder, it is something considered morally deprave, and so the Church would not recognize those actions of the people of the dark ages to be truly Christian, particularly since the Church isn't a scientific institution. Likewise, the actions of the pedophilic priests is also condemned by the Church. Such actions are deprave, and not condoned by the Church. Any attempt to ignore such actions would also be considered wrong by the Church.
The point is, humans are weak, both ignorant and yielding. Just because someone claims to believe in something, doesn't mean they understand what they say they believe, nor does it mean that they will follow that belief to the T. They SHOULD, I know. But the crude fact is that many, or even most, don't. If you are to judge a religion, judge it by it's teachings, and make sure those teachings are understood by you, so you can't simply read from a book, since words have many meanings. Teachings must be understood and explained, before a proper judgement can be made about anything. The concept of evolution, for example, is probably not understood by many people who condemn it. Furthermore, such condemners probably don't really understand what they believe anyway. Before one gives a "final judgement" about something, it must be considered until it is fully understood.
From speaking to you, Godless, it is clear that your notion of who and what God is, is based upon a misconception, a misconception that is entirely not your fault. It is the fault of those who hold the notion of God, but do not understand that notion themselves. So, by your understanding of God, as far as I can glean, I would also conclude that such a being couldn't possibly exist. However, my understanding of God is entirely different, and by it I have concluded that such a notion COULD, and probably does have reality.
So then the problem is this: Too many people believe in a false notion of God. Non-believers then remain as such, since such a notion is foolish, and believers with any wit would also see that misconcepted idea of God as foolish, and become non-believers themselves. Once someone, who has a clearer (though certainly not perfect) notion of who and what God is comes along, he/she is scoffed at because they are considered to have just "made up" another God among numerous that are already seen as silly. So their clearer conception of God is then dismissed without proper consideration. The problem is, GOD, as such, isn't getting proper consideration, and so a proper judgement on whether to believe in such a one is reasonable or otherwise isn't being made.