You just shifted invisibly from methodological naturalism (“science doesn’t deal with…”), an investigative choice, to metaphysical naturalism (“science doesn’t countenance…”), a metaphysical choice outside science. You also personify science, as if “it” could have metaphysical beliefs, rather than the human scientists who practise it - and of whom many, and nearly all its earllier practitioners, took the position that miracles have occurred, do occur, and will occur.
Your shift reminds me how easy it is, in practice, for naturalistic methodology to merge imperceptibly into naturalistic mindsets. Happens to Christian scientists too, many of whom feel an discomfort around the subject of miracles, as if suffering cognitive dissonance - but you can’t suffer such discomfort over a mere methodology.