Well, yes, where Religion is ONLY a tool for institutionalizing a Civilized Morality, then we can point out such contradictions as Religion seeming to condone what is ultimately an un-Civilized, anti-social act -- that of killing.
But Religion can be more than a Moral Vehicle. Indeed, Religion used to be entirely independent of Morality... or rather I should say that there was Religion long before there was the more precise versions of Morality that we appreciate today.
Indeed, this is why we often differentiate between the 'Higher' Religions and the more Ancient Religions and Philosophies. You see, the previous Religions did not have much of a moral sense to them. Religion was used to explain the Universe and the World, even to incorporate all of the apparent Evil and Injustice. Many of the Religious Philosophies traded off an Amoral Careless Apathy, which allowed for a wonderful Peace of Mind, for any anxiety about Morality and Suffering. Look it up and you will find that most Religions before Christ, Zoroaster and Buddha simply advised people not to worry about anything.
And even where Religion fronted for Civilization, then the emphasis was often more toward duty then toward any advanced notions of upholding Good in defense of Evil. We can see this in the Bhagavad Gita, of the Hindus, where their God, Krishna orchestrated a huge War, pushing both sides into the fray, explaining to everybody that the Interest of their Duties required the Conflict and that a Great Big War would be the only way he could imagine that a resolution could be arrived at. In this sense, Religion was actually a well documented Institutionalization of War, if not exactly for Civilization, well, at least as regards to the Aryan Brahmins, who were not really Civilized, but were in fact a Horde of Invading Barbarians from the North of India. What we call today, Caucasions.