The so-called Wars of Religion (1618-48) in Central Europe are often the touchstone for arguments in favour of keeping religion out of politics because of religion’s alleged ability to render politics violent. Yet, these wars are better understood as a series of disputes between rival princes seeking greater autonomy from the Holy Roman Emperor.
For long periods, Catholic France and the Catholic Hapsburgs were vehement enemies. Popes sometimes withdrew support for the Catholic Hapsburgs despite the common Protestant threat. Lutheran princes never attacked Calvinist princes despite heaps of rivalry, while Catholic/Protestant alliances flourished by the dozen. At one point, Catholic Spain supported the French (Protestant) Huguenots against France while Cardinal Richelieu himself would sign a treaty with Lutheran Sweden in 1631.
So, even at the height of these wars, religion was a background inconvenience, not the sole predictor of who would fight whom. And even where religion plays a more decisive role, it is not uniquely violent. The secularism of the French Revolution and the Christian support for the crusades are equally bloodthirsty. Envy and greed necessitate whatever ideological excuse along the road to plunder.