Science and religion are fundamentally in opposition. This is easily demonstrated.
While science is just an epistemology, and so might seem to be compatible with the metaphysics of religion, the basic epistemology of religion is exactly the opposite of science.
Science makes only three assumptions about the universe: that it is objective, that it is observable, and that it is consistent. Any metaphysics that embraces these three principles is compatible with science. The application of the epistemology of science requires skepticism and empiricism. It also requires the minimum possible assumptions. This is a tedious process, one that inherently recognizes that each result may be wrong, and assigns a measurement of the probability of correctness. In practice, this has given us a fundamental understanding of ourselves, the universe, and the reality around us.
Science is based on this: evidence first, tentative conclusion second, prediction of unknown evidence, testing of prediction. Wash, rinse, and repeat.
Religion, on the other hand, requires a lack of empiricism. It is an epistemology that encourages rational thought about irrational assumptions. This is because religion assumes the conclusion: that there is a god. Religion is predicated on this. It requires this assumption, and it requires that no evidence is necessary for this assumption.
These are two epistemologies that are diametrically opposed. The only way they can coexist is in with the metaphysical assumptions of theology, and well-compartmentalized. But when one encroaches on the other, they are in conflict.
They will always be in conflict.
This is because all religions make specific claims about the nature of reality. And the nature of reality is the purview of science. When a religion makes a specific claim about reality, science can test that claim. That is, after all, what science is good at. In fact, it's the only known successful epistemology for probing the nature of reality. So, science can test any claim religion makes about reality.
And religion must make specific claims about the nature of reality. Otherwise, the religion's god is impotent and worthless -- and then what's the point of it?
Morality? How does the assumption of the existence of a god contribute to morality? There's no way to probe the mind of this god without making even more irrational assumptions -- that this particular holy book is true, or that holy book is true. And then, are the laws laid down in the arbitrarily-chosen holy book really morality, or just law? How would you judge?
That's easy -- you'd judge based on whether or not it seemed moral. The same way people without religion judge morality.
Religion is, ultimately, a disjointed epistemology that can provide no real knowledge. Look at all the different religions in the world to see evidence of that simple truth. The epistemological framework of religion disposes of the exact things that make the epistemology of science successful -- the only way to gain knowledge is through the systematic observation of the attributes of reality.
So, yes. Religion and science are always in conflict. The fact that many people are able to compartmentalize these two opposing epistemologies doesn't negate that fact.