this post, but gets paid back 100-fold with all sorts of personal slurs at Coyne's blog (here and here). This is basically professional wrestling for the smart set.
But never mind the trappings. The underlying issue is about how well a person needs to know philosophy to decide what entities--like God--a "philosophically consistent scientist" can or can't believe in. The phrase, I take it, refers to someone who embraces both good science and good philosophy.
On the whole, I think the answer is that you need to know a lot. This is obvious when the ontology in question is more abstruse. Does the philosophically consistent scientist believe in abstract objects? Properties? Irreducible mentality? Causation? Ordinary objects? Tropes? Universals? Numbers? These are all hard questions of contemporary metaphysics. The more time you spend in philosophy, the better you can tell what counts as "good philosophy" about these questions.
The God question seems as if it's easier, because it's familiar. Everybody has an opinion about God, whereas few people have an opinion about abstract objects. Yet I think it's still true that more study means getting a better grip on what's good philosophy, and what isn't.
Is God allowed into an ontology compatible with good science and philosophy? Figuring it out raises lots of hard questions: Can there be entities that aren't part of the physical universe? Could God be somehow immanent in the physical universe? Does science require us to see the physical universe as a closed system, not disturbable "from outside"? Could a God who got the universe going, but never intervened again, be worth believing in?
A word about the last question. A God like that might be seen as having desires and preferences. Though "he" would not affect our world, our world would affect him--causing him pleasure and displeasure, admiration and outrage, etc. Believing this could motivate us to do some things and avoid others. Since the causation is "one way," nothing about the picture is inconsistent with the physical universe being closed and law governed.
Is it "good philosophy" to countenance a creator God who cares about us, but doesn't influence the physical universe? Well, I could make objections--i don't have the view in question. However, there are very highly regarded philosophers who do think this way. In light of that, it seems way too strong to say that any "philosophically consistent scientist" is forced to give up their faith. Accepting "good science" is much more directive than accepting "good philosophy"--philosophy being an area where the smartest, most capable people constantly disagree about almost everything.