“You gotta respect everyone’s beliefs.” NO, YOU DON’T. That’s what gets us in trouble: You have to acknowledge everyone’s beliefs. And then you have to reserve the right to go, “That’s fucking stupid, are you kidding me?”
— Patton Oswalt
You have to acknowledge their beliefs, and their right to hold them ... just before you burst out laughing. Because that which is ridiculous is worthy of ridicule. Particularly when it's demonstrably harmful.
I suppose that the debate comes in concerning what rises to the level of justified incivility (or even what constitutes incivility). Hatred of gays, mistreatment of refugees, and other clear harms are certainly not due any deference or free pass. Simple disagreement is certainly not uncivil.
So I would say, matter of fact disagreement and statement of reasons why is always acceptable; undisguised derision and disgust for ideology that is clearly harmful to others is also acceptable. Assuming a person is harmful just for believing in god ... that is no better than a believer assuming we're evil just because we don't.