It seems to me that there are at least two options open.
Firstly from all bu the most liberal Christian view it is clear that God must intervene openly in human history - but that does not necessarily mean that there are such interventions - at least that we could detect in the overall history of life on Earth.
Then there is the view that God sustains and operates through the natural order - that there is no separation between the actions of nature and those of God.
Both of these allow the methodological naturalism of science without taking the further step into philosophical naturalism. Both place themselves outside Lewis'criticism - they leave a place for forces beyond naturalism but they do so by faith. And that is what is unacceptable to Dembski. Dembski demands a God whose existence is demonstrable - and moreover demands that the evidence for that demonstration must exist.