Science doesn't need metaphysical naturalism to work. One could change every "law" of physics to say "given X, God does Y". The problem is that there is zero difference between that and a statement that does not include God.
If the world included magic, science would be able to study it. If it included miracles, science would be able to identify them and categorize under what conditions they happened, and create hypotheses about what might induce another "miracle" to happen.
If there is a deity who futzes around with reality only when people aren't looking, and hides all evidence of it, then we are in trouble. But then, so are the theists, who must explain why such a deity exists, and how they know anything about it.
If the world included magic, science would be able to study it. If it included miracles, science would be able to identify them and categorize under what conditions they happened, and create hypotheses about what might induce another "miracle" to happen.
If there is a deity who futzes around with reality only when people aren't looking, and hides all evidence of it, then we are in trouble. But then, so are the theists, who must explain why such a deity exists, and how they know anything about it.