I see what you're trying to do here, and will watch your work with great interest! Two thoughts:

1) If you align yourself with the cause of the day, and then that cause fails, then you fail with it.

2) Is it not really, in the end, all about power and not ideology? Whatever logical arguments you use are mere window-dressing to give an air of respectability. I imagine, in your example of the Middle Ages, that you would find yourself simply ignored by those in power until you were able to credibly threaten their power or increase their power, at which point you would be destroyed / assimilated as those in power saw fit. This result would be 100% uncorrelated with whatever you're saying, whether it was deeply heretical to Christianity or an unimpeachable logical consequence of the core tenets of the religion.

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