This is a common misunderstanding. First of all, there is not unanimous agreement among philosophers of science that methodological naturalism is a necessary aspect of the scientific method. But that aside, MN does not mean that, even there was rock solid, undeniable evidence for the existence of Gods, angels, demons, and other beings usually described as “supernatural”, someone adhering to the scientific method would have to ignore this evidence because he is not allowed to consider such entities when performing science.
Rather, MN means that if evidence exists for the existence of such beings, they would be considered to be aspects of the natural world and incorporated into our understanding of it. They would not be separated off into their own category or compartment called “supernatural” and considered to be exempt from the laws and principles that govern the “natural world.” Instead, our understanding of the laws and principles governing the “natural world” would have to be changed to accommodate what we understand about these beings.
Which is to say that those who properly adhere to the scientific method do not dismiss the existence of gods, angels and demons because the rules of science require this. Rather, their existence is dismissed because of the lack of evidence supporting their existence.