Christianity is compatible with (and even demands) some rational theist doctrines and is incompatible with others. Philosophical theism has been used as a perfectly fine club to beat Christianity with- and it makes a better club than atheism or naturalism.
There are three steps in the hierarchy of natural doctrines opposed to Christianity 1.) A naturalism that doesn’t even bother to take what Christianity is about seriously, but insists its object is in every way a pure illusion of ignorance and/ or stupidity 2.) A naturalism that takes the object seriously, though it denies such an object exists, and tries to explain the desire for this object as a misplaced desire for something else (Feuerbach, Marx) 3.) A robust philosophical theism (or natural pluralist religion) that sets itself against Christianity or “religion” while still admitting the reality of some of the objects the Christian holds to exist (an absolute, an afterlife, mystical experience, etc.)
Christianity can present wildly different (though very compatible) visions of itself depending on which of the above three is dominant in a given culture. We are all quite familiar with #1, and so we tend towards defenses that would be particularly vulnerable to #3; other times (say, 1750-1870- think of Kant- or the time of John Damascene vs. the Arians) were more familiar with #3, and so they tended to stress the mysterious character of Christianity.