I have always found this objection somewhat puzzling. To wage war over religion is to wage war over:

• What is true of the world
• What is required of mankind
• How society and its resources should therefore be organised

To be clear, this is the only thing we fight about. Take even the simplest territorial contest. The dispute necessarily starts from a distinction between “us” and “them”. How can this distinction be made, but for conclusions on the above questions? Whether “they” are of a different colour, family, origin, politics or history, it is ideology alone which makes these differences relevant. All disputes of ownership are essentially ideological. “That is mine” is not an isolated statement, but one tailed by a whole army of thoughts, about what is true of the world, what is required of mankind, and how things should therefore be organised.

Given this, the objection that religion causes war can only mean one of a number of puzzling things.

• It could mean that religious wars are particularly heinous, and that it would be more noble to shed blood over ideologies of a different kind; perhaps simpler ideologies, unsullied by haughty claims to the divine. But to extract the divine from a possessive claim is not necessarily to make it any more sensible or admirable. “That should be mine because I find it shiny” seems even worse than “that should be mine because the gods above would have it so.”
• Second, it could mean that all religions are false and so ought not to be fought about, because neither side can possibly be right in their fighting. This may be true, but the matter cannot be settled in advance. We cannot say that religion is false because it makes dishonourable wars, and that its wars are dishonourable because religion is false.
• Third, it could mean that we would have far fewer wars if there were no religious disputes, and that religion should therefore be done away with in protection of human life. But to begin with, wars with religious causes account for about 2% of conflict-related deaths. More pertinently, this objection essentially says that there would be far fewer wars if people just agreed more about how the world is and how it should be. This is just trivially true, and not remotely interesting. It says very little about war and very little about religion.
• Fourth, it could mean that far fewer wars would occur if we simply agreed on one religious conclusion: that there is no God. Sure. But even fewer wars than that would occur if we simply agreed that wars were a terrible idea, and such strict pacifism is more likely to hail from Jainists than atheists. Should we be Jainists then? Not if there is no good evidence that Jainism is true. As for atheism and as for the rest.
• Fifth, it could mean that war is an evil and no true religion would command it. But then let us say that all religions which command war are false, and argue for that theological view, with considerable philosophical theology to back ourselves. We have not defeated religion, then, for there are millions of us pacifist theists about the place, and indeed if we were all pacifist theists, we would all do far better against the evils of war. This objection could just as easily call for more religion as it could call for less.

These readings are only subtly different, but whatever else wars are about, they are fundamentally fought over truth and falsehood. Socialism offers one take, nationalism another, Christianity another, Islam another, Judaism another. But Christianity, Islam and Judaism, cannot be grouped here. The theistic ideologies and the atheistic ideologies alike propose answers to precisely the same questions, and it is disagreement on those questions which beckons knights and soldiers.