You toe the line of a dialectic between faith and reason--a very useful dispute. It assumes the two positions of faith and reason as fundamental. This is the position you have pounded into your head and tout it when you want it so: "the two will always be in conflict." But when useful, you will be monist, for in your world reason must be ascendant, except when chance happens to show up, whatever that is.
You say: The fact of the matter is it was logic and reason, not religion that are the parents of science. Huh? What is a parent? A genesis? Is this a metaphor interrupting the order of logic? Are you trying to say history is logic? Get this straightened out before you confuse all these bumbling posters who are under your poetic tutelage. Historically, religion was inseparable from the birth of science--prior to Socrates and Plato, both of whom retained a profound understanding of the limits of logic. But better not talk about Plato for he would pound your arrogance: "Oh well, answered my own question." Aristotle then? No, you want to talk about Aquinas while arguing for the parents of science. Your argument is framed anachronistically. When exactly was science born? When? And if reason and logic are the parents, who gave birth to religion? Is this genealogy of yours--this parentage of logic and reason-- is this what you call a post hoc ergo propter hoc fallacy? For sure this is a mass confusion, a confusion very typical of today's journalism, most of which is propaganda.
Religion has fought every scientific advance, every step along the way. Yeah right.. This is so demonstrably false. OK class, back to logic 101: "All men are wise" and "All cows are brown" etc? What you should have said is religion has fought scientific advance. Or, science has fought religious advance. Both are historically true. And this one is true too: you fight religion at the expense of logic and history.
If evolution is proven correct, God is disproven. Only if you are a monist belonging to your school. Draw the map of reality and you can prove anything. Anything. You can even prove or disprove your own existence--as you wish, draw your map. *God forgive these Creationist shysters for doing the same.*
It was the womb of Christianity that kept Europe in the horror of the Dark Ages for a millennia. All I will answer to that is this 
Aquinas made the mistake of trying to logically prove the existence of God False. He did no such thing. I see so many statements from ignorance. One thing that Aquinas did read was Aristotle. Aristotle said first principles are not proven. Can't be proven. The five ways make God's existence logically consistent. You see, Aquinas does not share your dualistic monism. He will not make logic the cause of existence, as in the Cartesian method. He will not make logic the first principle. (Dataman caught you on this). In your world, reason = existence. Therefore, anything that reason proves, exists. All else is antithetical (and on a better day, non-existent by insistence). And if the likes of you had lived at the time of Aquinas, they would have begun with your first premise and ended up proving existence from your logic. In other words you would do exactly what you claim Aquinas failed to do. But he did no such thing. You might rather join up with Abelard.
the moral influence of the concept of God was falling away from Europe. And you say, this proved true. What are you proving? To use your language: what also proved true was the rise of Christianity, whether Nietzsche postdicted it or not. What's your point? Is your monism a deterministic fallacy of the Latin kind? post hoc ergo propter hoc?
And now, just like Marx and Nietzsche (famous conservatives!) you try to answer to the problem of creating an ersatz morality. And like Nietzsche and Foucault, you argue that all what the others want is control. To which the words of Bob Dylan: "you gotta serve somebody." And you call in reason like a self-service station. How convenient. In your world, otherness does not exist as it makes way for your expansive reason, fueled by you high octane will.
you cannot do anything for yourself, only for others. Thus one is a complete slave to others. This is in utter contradiction to the principle of Capitalism, which holds one is responsible to oneself, for oneself. Here's where your dualism springs up again. Logically, a contradiction. But why ought the existence of otherness or plurality be a contradiction. Why does your monism push against your dualism? Why does the service to another logically (or did you want to argue existentically?) negate the existence of the self? Or vice versa? All this springs from your dualistic conundrum coming under a monistic domination of LogicWing's reason. The twisting and the convolutions that your logic goes through attempts to disprove the unprovable and while asserting the unprovable as the provable. This self-destructs the concepts of logic, facts and reason in the process because it reduces existence to thought. Read your Aristotle. Read your Kant: a hundred dollars in your mind don't put any in your pocket. The inability to see the fallacies inherent your accusations is the same inability to understand what has occurred in the history of logical thinking.