[Abrahamic Religions] religion as authoritarian ideology? Can religion really coexist with a nation-state?

From my own experience, it seems that "good" is defined as "God's will" and "bad" is everything outside and/or opposed to it.

(Of course, the group I'm currently meeting with [and really, really wanna flip the bird at] defines good as God Himself and bad as anything that comes from ourselves. [in practice meaning that actions taken while walking in the Spirit are good and that anything that originates from our natural self is bad]. But enough about that.)

Back to the point, it appears that adherents to monotheist religions that follow an all-powerful entity define their morality as following the will and desires of one individual sentient intelligence. One intelligence defines what is "good" and "evil" according to its personal desires and values, and mandates that it followers share those values in order to remain in its good graces, while also (falsely) portraying the good and evil it defines as universal and objective.

I'm having trouble seeing this as anything but a political entity akin to an authoritarian or totalitarian regime. Is this an apt description or am I mistaken?

(I suppose my current distaste not just for my church but also for the idea of god is that I hate authoritarians of all shapes and sizes. I believe that if I had their livers on my plate, the world would be a better place for it, assuming that more egalitarian and equitable regimes take their place.)

This leads to the question I want to ask: I am currently struggling with the extreme tangent of thought that anybody who subscribes to this sort of religion or interpretation of a religion should be considered an enemy of the state, as their primary loyalty lies with a political entity that is not the nation-state. I know many who place adherence to God's law over adherence towards the law of the land. Granted, the only governments in this day and age who would get really nitpicky about this would be the aforementioned authoritarians (as seen in heavily enforced state religions and/or atheism), but when in the realm of ideas, it would seem that belief and obedience of a god such as the one described in the Bible would be a threat to the sovereignty and laws of any given human nation. Why aren't heavily religious people in positions of power treated the same as a foreign spy in a position of power whose true loyalty was discovered? Aren't they interfering with proper political process by owing their chief loyalty not to the state, but to an entity outside of it with its own laws and sovereignty?