There is a rather glaring difference here: the means. ISIS believes in converting by force, and killing those that don’t conform. Christian groups believe in converting through acts of charity and persuasion. Not exactly in the same ballpark mate.
Many evangelical people may support a legal system that criminalizes behavior they view as sinful, but by no measure of the imagination are they proposing wholesale slaughter or enslavement based on religious affiliation.
Your article actually does say a lot of things I agree with, particularly about the merits of separating church and state — then you go off on the ISIS/ taliban comparison. A shame. It might have been a productive article otherwise.