I tend to like Sean Carroll’s view expressed in his recent book The Big Picture: On the Origins of Life, Meaning, and the Universe Itself :
Science should be interested in determining the truth, whatever that truth may be – natural, supernatural, or otherwise. The stance known as methodological naturalism, while deployed with the best of intentions by supporters of science, amounts to assuming part of the answer ahead of time. If finding truth is our goal, that is just about the biggest mistake we can make.