As Sy suggests, my own take on MN is that we should ditch the artificial and unbiblical Enlightenment division between the "natural" and the "supernatural", because "natural" is such a fluid concept.,, and no longer easily definable now science has ditched the early-modern "mechanical philosophy" of inert matter and God-given laws.
Gravity had to be redefined as "natural" after Newton, though science had for a century or more rejected "occult" forces acting at a distance as definitionally supernatural. In our own age, the current paradigm deals very badly with concepts like "mind" (which many quantum theorists see as essential a component of natural reality as matter) and the linked concept of "information", which is clearly immaterial, though equally clearly a part of nature, and especially of life.
Teleology, too, was originally excluded from science by Bacon as (a) supernatural if extrinsic and (b) dishonouring to God's honour if intrinsic. But now it is increasingly clearly a real part of nature - so on what principle are final and formal causes still excluded from scientific methodology?
MN even reduces the concept of matter to a mystical duality, where "natural" simply seems to mean "expressible in mathematical equations".
Theologically speaking, as we move away from Enlightenment deism, those in the science-faith dialogue have to reclaim a relationship between God's daily providence (a core doctrine of truly Christian theism) and science: if God answers prayer for our daily bread, and governs history, then there ought to be at least for Christian scientists some concept of how that works, lest the familiar tendency of letting methodological naturalism encroach on our metaphysics and theology will always cause problems. I suggested one possibility here.
We also have to reclaim a proper theological understanding of randomness, given that under MN the proper scientific definition of "unpredictable" (cf Donald MacKay on this) is routinely extended to mean "causeless", even by some ECs - that is done both by biologists opposing evolution to divine creation, and by physicists who say that quantum events are acausal. For the Christian whose metaphysics is theistic, the idea of God's causing something that has no cause ought to be seen as no less incoherent than his creating a square circle.
Note that all this has nothing to do with miracles - the biblical picture of the natural creation is not of an autonomous nature being occasionally nudged by "interfering" miracles, but of a household constantly guided by God's supervision and management. Yet miracles (exceptional events) do occur, now as in Jesus's ministry. It is easy to neglect that, in the mathematical sense that they are negligibly rare, in the natural sciences, on the assumption (a theological assumption, rather than a scientific one) that nature has always been essentially a self-contained system.
But as I point out in a recent post, there are some scientific disciplines - notably medicine - where claims of the miraculous can only be sidelined by ignoring the data, or by insisting on interpreting it as if one were a metaphysical, rather than a methodological, naturalist. The believing scientist should not, surely, have to deny the remarkable works of God as if his professional methodology applied to the whole of life.