Unfortunately for Prager's argument, there are too many examples of past Christian misuse of religion which simply cannot be handwaved away in this manner (e.g. church agitation for prohibition, which is an unbreakable analogy since it concerns the exact same act: possession of alcohol).
Sorry. There were plenty o' Christian folks against Prohibition. There just more on the wrong side of the equation. And we solved it without sawing anybody's heads off...