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Will, the first argument you make seems to boil down to "In this one specific instance, some religious people are seeking to stall scientific progress; therefore, religion in general necessarily stalls scientific progress." Of course, this is not a valid argument.
Your second argument is that, because religions presuppose the existence of miracles, they necessarily stall scientific progress, because the existence of miracles contradicts science. This is true in one sense, but false in another. If you view the laws of science as immutable truths that cannot be overriden, then yes, religions (at least, Christianity) contradict science. I'll apparently be continuing this later.
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"Die Deutschen meinen, daß die Kraft sich in Härte und Grausamkeit offenbaren müsse, sie unterwerfen sich dann gerne und mit Bewunderung:[...]. Daß es Kraft giebt in der Milde und Stille, das glauben sie nicht leicht."
"The Germans believe that power must reveal itself in hardness and cruelty and then submit themselves gladly and with admiration[...]. They do not believe readily that there is power in meekness and calm."
-- Friedrich Nietzsche
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