Religion must be accepted as a source of energy. It can be directed for our purposes, but only within limits that experience reveals. Here is the secret meaning of Free Will.
Enter no conflict against fanatics unless you can defuse them. Oppose a religion with another religion only if your proofs (miracles) are irrefutable or if you can mesh in a way that the fanatics accept you as god-inspired. This has long been the barrier to science assuming a mantle of divine revelation. Science is so obviously manmade. Fanatics (and many are fanatic on one subject or another) must know where you stand, but more important, must recognize who whispers in your ear.