ToE has been used by naturalists to attack Christianity. That is most assuredly correct. But the science behind what ToE has morphed into today is not a philosophy. It's based on the scientific method. Hypothesis, Observation.Testing, Conclusion. And it, through many hiccups and sideroads, has become the dominant, most rational for the data, explanation based on experiment (not faith) out there today. That's what good science does. It preens out the crap over time and only the ideas that stand the test of time and repeated questioning remain. See Newton's Laws and Maxwell's Equations...
This is actually the fallacy of affirming the consequent. That because P 'predicts' Q and Q is observed; then P is supported. This works if and only if all alternatives to P are proved to be impossible.
The philosophy of naturalism is what forces 'science' to conclude that what is observed happened without cause and for no reason through purely natural methods. Alternatives to P are excluded by definition. This is a philosophical choice, a scientific axiom, not an empirical fact.